diff --git a/crates/api/src/externals.rs b/crates/api/src/externals.rs
index 576c92e15e..43639cacc1 100644
--- a/crates/api/src/externals.rs
+++ b/crates/api/src/externals.rs
@@ -1,7 +1,8 @@
-use crate::trampoline::{generate_global_export, generate_memory_export, generate_table_export};
+use crate::trampoline::{
+    generate_global_export, generate_memory_export, generate_table_export, StoreInstanceHandle,
+};
 use crate::values::{from_checked_anyfunc, into_checked_anyfunc, Val};
-use crate::Mutability;
-use crate::{ExternType, GlobalType, MemoryType, TableType, ValType};
+use crate::{ExternType, GlobalType, MemoryType, Mutability, TableType, ValType};
 use crate::{Func, Store, Trap};
 use anyhow::{anyhow, bail, Result};
 use std::slice;
@@ -92,21 +93,20 @@ impl Extern {
 
     pub(crate) fn from_wasmtime_export(
         wasmtime_export: wasmtime_runtime::Export,
-        store: &Store,
-        instance_handle: InstanceHandle,
+        instance: StoreInstanceHandle,
     ) -> Extern {
         match wasmtime_export {
             wasmtime_runtime::Export::Function(f) => {
-                Extern::Func(Func::from_wasmtime_function(f, store, instance_handle))
+                Extern::Func(Func::from_wasmtime_function(f, instance))
             }
             wasmtime_runtime::Export::Memory(m) => {
-                Extern::Memory(Memory::from_wasmtime_memory(m, store, instance_handle))
+                Extern::Memory(Memory::from_wasmtime_memory(m, instance))
             }
             wasmtime_runtime::Export::Global(g) => {
-                Extern::Global(Global::from_wasmtime_global(g, store, instance_handle))
+                Extern::Global(Global::from_wasmtime_global(g, instance))
             }
             wasmtime_runtime::Export::Table(t) => {
-                Extern::Table(Table::from_wasmtime_table(t, store, instance_handle))
+                Extern::Table(Table::from_wasmtime_table(t, instance))
             }
         }
     }
@@ -114,9 +114,9 @@ impl Extern {
     pub(crate) fn comes_from_same_store(&self, store: &Store) -> bool {
         let my_store = match self {
             Extern::Func(f) => f.store(),
-            Extern::Global(g) => &g.store,
-            Extern::Memory(m) => &m.store,
-            Extern::Table(t) => &t.store,
+            Extern::Global(g) => &g.instance.store,
+            Extern::Memory(m) => &m.instance.store,
+            Extern::Table(t) => &t.instance.store,
         };
         Store::same(my_store, store)
     }
@@ -163,9 +163,8 @@ impl From<Table> for Extern {
 /// instances are equivalent in their functionality.
 #[derive(Clone)]
 pub struct Global {
-    store: Store,
+    instance: StoreInstanceHandle,
     wasmtime_export: wasmtime_runtime::ExportGlobal,
-    wasmtime_handle: InstanceHandle,
 }
 
 impl Global {
@@ -187,11 +186,10 @@ impl Global {
         if val.ty() != *ty.content() {
             bail!("value provided does not match the type of this global");
         }
-        let (wasmtime_handle, wasmtime_export) = generate_global_export(store, &ty, val)?;
+        let (instance, wasmtime_export) = generate_global_export(store, &ty, val)?;
         Ok(Global {
-            store: store.clone(),
+            instance,
             wasmtime_export,
-            wasmtime_handle,
         })
     }
 
@@ -246,7 +244,7 @@ impl Global {
         if val.ty() != ty {
             bail!("global of type {:?} cannot be set to {:?}", ty, val.ty());
         }
-        if !val.comes_from_same_store(&self.store) {
+        if !val.comes_from_same_store(&self.instance.store) {
             bail!("cross-`Store` values are not supported");
         }
         unsafe {
@@ -264,13 +262,11 @@ impl Global {
 
     pub(crate) fn from_wasmtime_global(
         wasmtime_export: wasmtime_runtime::ExportGlobal,
-        store: &Store,
-        wasmtime_handle: InstanceHandle,
+        instance: StoreInstanceHandle,
     ) -> Global {
         Global {
-            store: store.clone(),
+            instance,
             wasmtime_export,
-            wasmtime_handle,
         }
     }
 }
@@ -292,18 +288,17 @@ impl Global {
 /// instances are equivalent in their functionality.
 #[derive(Clone)]
 pub struct Table {
-    store: Store,
-    wasmtime_handle: InstanceHandle,
+    instance: StoreInstanceHandle,
     wasmtime_export: wasmtime_runtime::ExportTable,
 }
 
 fn set_table_item(
-    handle: &InstanceHandle,
+    instance: &InstanceHandle,
     table_index: wasm::DefinedTableIndex,
     item_index: u32,
     item: wasmtime_runtime::VMCallerCheckedAnyfunc,
 ) -> Result<()> {
-    handle
+    instance
         .table_set(table_index, item_index, item)
         .map_err(|()| anyhow!("table element index out of bounds"))
 }
@@ -322,18 +317,17 @@ impl Table {
     /// Returns an error if `init` does not match the element type of the table.
     pub fn new(store: &Store, ty: TableType, init: Val) -> Result<Table> {
         let item = into_checked_anyfunc(init, store)?;
-        let (wasmtime_handle, wasmtime_export) = generate_table_export(store, &ty)?;
+        let (instance, wasmtime_export) = generate_table_export(store, &ty)?;
 
         // Initialize entries with the init value.
         let definition = unsafe { &*wasmtime_export.definition };
-        let index = wasmtime_handle.table_index(definition);
+        let index = instance.table_index(definition);
         for i in 0..definition.current_elements {
-            set_table_item(&wasmtime_handle, index, i, item.clone())?;
+            set_table_item(&instance, index, i, item.clone())?;
         }
 
         Ok(Table {
-            store: store.clone(),
-            wasmtime_handle,
+            instance,
             wasmtime_export,
         })
     }
@@ -345,10 +339,7 @@ impl Table {
     }
 
     fn wasmtime_table_index(&self) -> wasm::DefinedTableIndex {
-        unsafe {
-            self.wasmtime_handle
-                .table_index(&*self.wasmtime_export.definition)
-        }
+        unsafe { self.instance.table_index(&*self.wasmtime_export.definition) }
     }
 
     /// Returns the table element value at `index`.
@@ -356,8 +347,8 @@ impl Table {
     /// Returns `None` if `index` is out of bounds.
     pub fn get(&self, index: u32) -> Option<Val> {
         let table_index = self.wasmtime_table_index();
-        let item = self.wasmtime_handle.table_get(table_index, index)?;
-        Some(from_checked_anyfunc(item, &self.store))
+        let item = self.instance.table_get(table_index, index)?;
+        Some(from_checked_anyfunc(item, &self.instance.store))
     }
 
     /// Writes the `val` provided into `index` within this table.
@@ -368,8 +359,8 @@ impl Table {
     /// the right type to be stored in this table.
     pub fn set(&self, index: u32, val: Val) -> Result<()> {
         let table_index = self.wasmtime_table_index();
-        let item = into_checked_anyfunc(val, &self.store)?;
-        set_table_item(&self.wasmtime_handle, table_index, index, item)
+        let item = into_checked_anyfunc(val, &self.instance.store)?;
+        set_table_item(&self.instance, table_index, index, item)
     }
 
     /// Returns the current size of this table.
@@ -387,12 +378,11 @@ impl Table {
     /// error if `init` is not of the right type.
     pub fn grow(&self, delta: u32, init: Val) -> Result<u32> {
         let index = self.wasmtime_table_index();
-        let item = into_checked_anyfunc(init, &self.store)?;
-        if let Some(len) = self.wasmtime_handle.clone().table_grow(index, delta) {
-            let mut wasmtime_handle = self.wasmtime_handle.clone();
+        let item = into_checked_anyfunc(init, &self.instance.store)?;
+        if let Some(len) = self.instance.table_grow(index, delta) {
             for i in 0..delta {
                 let i = len - (delta - i);
-                set_table_item(&mut wasmtime_handle, index, i, item.clone())?;
+                set_table_item(&self.instance, index, i, item.clone())?;
             }
             Ok(len)
         } else {
@@ -414,7 +404,7 @@ impl Table {
         src_index: u32,
         len: u32,
     ) -> Result<()> {
-        if !Store::same(&dst_table.store, &src_table.store) {
+        if !Store::same(&dst_table.instance.store, &src_table.instance.store) {
             bail!("cross-`Store` table copies are not supported");
         }
 
@@ -423,10 +413,10 @@ impl Table {
         // come from different modules.
 
         let dst_table_index = dst_table.wasmtime_table_index();
-        let dst_table = dst_table.wasmtime_handle.get_defined_table(dst_table_index);
+        let dst_table = dst_table.instance.get_defined_table(dst_table_index);
 
         let src_table_index = src_table.wasmtime_table_index();
-        let src_table = src_table.wasmtime_handle.get_defined_table(src_table_index);
+        let src_table = src_table.instance.get_defined_table(src_table_index);
 
         runtime::Table::copy(dst_table, src_table, dst_index, src_index, len)
             .map_err(Trap::from_jit)?;
@@ -435,12 +425,10 @@ impl Table {
 
     pub(crate) fn from_wasmtime_table(
         wasmtime_export: wasmtime_runtime::ExportTable,
-        store: &Store,
-        wasmtime_handle: wasmtime_runtime::InstanceHandle,
+        instance: StoreInstanceHandle,
     ) -> Table {
         Table {
-            store: store.clone(),
-            wasmtime_handle,
+            instance,
             wasmtime_export,
         }
     }
@@ -654,8 +642,7 @@ impl Table {
 /// [open an issue]: https://github.com/bytecodealliance/wasmtime/issues/new
 #[derive(Clone)]
 pub struct Memory {
-    store: Store,
-    wasmtime_handle: InstanceHandle,
+    instance: StoreInstanceHandle,
     wasmtime_export: wasmtime_runtime::ExportMemory,
 }
 
@@ -683,11 +670,10 @@ impl Memory {
     /// # }
     /// ```
     pub fn new(store: &Store, ty: MemoryType) -> Memory {
-        let (wasmtime_handle, wasmtime_export) =
+        let (instance, wasmtime_export) =
             generate_memory_export(store, &ty).expect("generated memory");
         Memory {
-            store: store.clone(),
-            wasmtime_handle,
+            instance,
             wasmtime_export,
         }
     }
@@ -827,22 +813,19 @@ impl Memory {
     /// ```
     pub fn grow(&self, delta: u32) -> Result<u32> {
         let index = self
-            .wasmtime_handle
+            .instance
             .memory_index(unsafe { &*self.wasmtime_export.definition });
-        self.wasmtime_handle
-            .clone()
+        self.instance
             .memory_grow(index, delta)
             .ok_or_else(|| anyhow!("failed to grow memory"))
     }
 
     pub(crate) fn from_wasmtime_memory(
         wasmtime_export: wasmtime_runtime::ExportMemory,
-        store: &Store,
-        wasmtime_handle: wasmtime_runtime::InstanceHandle,
+        instance: StoreInstanceHandle,
     ) -> Memory {
         Memory {
-            store: store.clone(),
-            wasmtime_handle,
+            instance,
             wasmtime_export,
         }
     }
diff --git a/crates/api/src/func.rs b/crates/api/src/func.rs
index 98d1e54704..ac1838a5e4 100644
--- a/crates/api/src/func.rs
+++ b/crates/api/src/func.rs
@@ -1,3 +1,5 @@
+use crate::runtime::StoreInner;
+use crate::trampoline::StoreInstanceHandle;
 use crate::{Extern, FuncType, Memory, Store, Trap, Val, ValType};
 use anyhow::{bail, ensure, Context as _, Result};
 use std::cmp::max;
@@ -5,6 +7,7 @@ use std::fmt;
 use std::mem;
 use std::panic::{self, AssertUnwindSafe};
 use std::ptr;
+use std::rc::Weak;
 use wasmtime_runtime::{Export, InstanceHandle, VMContext, VMFunctionBody};
 use wasmtime_runtime::{ExportFunction, VMTrampoline};
 
@@ -135,8 +138,7 @@ use wasmtime_runtime::{ExportFunction, VMTrampoline};
 /// ```
 #[derive(Clone)]
 pub struct Func {
-    store: Store,
-    instance: InstanceHandle,
+    instance: StoreInstanceHandle,
     export: ExportFunction,
     trampoline: VMTrampoline,
 }
@@ -176,7 +178,7 @@ macro_rules! getters {
             // of the closure. Pass the export in so that we can call it.
             let instance = self.instance.clone();
             let export = self.export.clone();
-            let max_wasm_stack = self.store.engine().config().max_wasm_stack;
+            let max_wasm_stack = self.store().engine().config().max_wasm_stack;
 
             // ... and then once we've passed the typechecks we can hand out our
             // object since our `transmute` below should be safe!
@@ -236,7 +238,7 @@ impl Func {
         ty: FuncType,
         func: impl Fn(Caller<'_>, &[Val], &mut [Val]) -> Result<(), Trap> + 'static,
     ) -> Self {
-        let store_clone = store.clone();
+        let store_weak = store.weak();
         let ty_clone = ty.clone();
 
         // Create our actual trampoline function which translates from a bunch
@@ -255,7 +257,7 @@ impl Func {
             let mut returns = vec![Val::null(); ty_clone.results().len()];
             func(
                 Caller {
-                    store: &store_clone,
+                    store: &store_weak,
                     caller_vmctx,
                 },
                 &args,
@@ -281,7 +283,6 @@ impl Func {
         let (instance, export, trampoline) =
             crate::trampoline::generate_func_export(&ty, func, store).expect("generated func");
         Func {
-            store: store.clone(),
             instance,
             export,
             trampoline,
@@ -483,6 +484,7 @@ impl Func {
         // Signatures should always be registered in the store's registry of
         // shared signatures, so we should be able to unwrap safely here.
         let sig = self
+            .instance
             .store
             .compiler()
             .signatures()
@@ -498,6 +500,7 @@ impl Func {
     /// Returns the number of parameters that this function takes.
     pub fn param_arity(&self) -> usize {
         let sig = self
+            .instance
             .store
             .compiler()
             .signatures()
@@ -509,6 +512,7 @@ impl Func {
     /// Returns the number of results this function produces.
     pub fn result_arity(&self) -> usize {
         let sig = self
+            .instance
             .store
             .compiler()
             .signatures()
@@ -549,7 +553,7 @@ impl Func {
             if arg.ty() != *ty {
                 bail!("argument type mismatch");
             }
-            if !arg.comes_from_same_store(&self.store) {
+            if !arg.comes_from_same_store(&self.instance.store) {
                 bail!("cross-`Store` values are not currently supported");
             }
             unsafe {
@@ -561,7 +565,7 @@ impl Func {
         if let Err(error) = unsafe {
             wasmtime_runtime::catch_traps(
                 self.export.vmctx,
-                self.store.engine().config().max_wasm_stack,
+                self.instance.store.engine().config().max_wasm_stack,
                 || {
                     (self.trampoline)(
                         self.export.vmctx,
@@ -593,8 +597,7 @@ impl Func {
 
     pub(crate) fn from_wasmtime_function(
         export: wasmtime_runtime::ExportFunction,
-        store: &Store,
-        instance: InstanceHandle,
+        instance: StoreInstanceHandle,
     ) -> Self {
         // Each function signature in a module should have a trampoline stored
         // on that module as well, so unwrap the result here since otherwise
@@ -607,7 +610,6 @@ impl Func {
             instance,
             export,
             trampoline,
-            store: store.clone(),
         }
     }
 
@@ -734,7 +736,7 @@ impl Func {
     }
 
     pub(crate) fn store(&self) -> &Store {
-        &self.store
+        &self.instance.store
     }
 }
 
@@ -970,7 +972,23 @@ pub trait IntoFunc<Params, Results> {
 /// the caller's memory until interface types has been fully standardized and
 /// implemented.
 pub struct Caller<'a> {
-    store: &'a Store,
+    // Note that this is a `Weak` pointer instead of a `&'a Store`,
+    // intentionally so. This allows us to break an `Rc` cycle which would
+    // otherwise look like this:
+    //
+    // * A `Store` object ...
+    // * ... owns all `InstanceHandle` objects ...
+    // * ... which are created in `Func::wrap` with custom host data ...
+    // * ... where the custom host data needs to point to `Store` to be stored
+    //   here
+    //
+    // This `Rc` cycle means that we would never actually reclaim any memory or
+    // deallocate any instances. To break this cycle we use a weak pointer here
+    // which points back to `Store`. A `Caller` should only ever be usable
+    // when the original `Store` is alive, however, so this should always be an
+    // upgrade-able pointer. Alternative solutions or other ideas to break this
+    // cycle would be most welcome!
+    store: &'a Weak<StoreInner>,
     caller_vmctx: *mut VMContext,
 }
 
@@ -1004,7 +1022,14 @@ impl Caller<'_> {
                 Some(Export::Memory(m)) => m,
                 _ => return None,
             };
-            let mem = Memory::from_wasmtime_memory(export, self.store, instance);
+            // Our `Weak` pointer is used only to break a cycle where `Store`
+            // stores instance handles which have this weak pointer as their
+            // custom host data. This function should only be invoke-able while
+            // the `Store` is active, so this upgrade should always succeed.
+            debug_assert!(self.store.upgrade().is_some());
+            let handle =
+                Store::from_inner(self.store.upgrade()?).existing_instance_handle(instance);
+            let mem = Memory::from_wasmtime_memory(export, handle);
             Some(Extern::Memory(mem))
         }
     }
@@ -1057,8 +1082,8 @@ macro_rules! impl_into_func {
                         // Double-check ourselves in debug mode, but we control
                         // the `Any` here so an unsafe downcast should also
                         // work.
-                        debug_assert!(state.is::<(F, Store)>());
-                        let (func, store) = &*(state as *const _ as *const (F, Store));
+                        debug_assert!(state.is::<(F, Weak<StoreInner>)>());
+                        let (func, store) = &*(state as *const _ as *const (F, Weak<StoreInner>));
                         panic::catch_unwind(AssertUnwindSafe(|| {
                             func(
                                 Caller { store, caller_vmctx },
@@ -1102,7 +1127,7 @@ macro_rules! impl_into_func {
                 let mut ret = Vec::new();
                 R::push(&mut ret);
                 let ty = FuncType::new(_args.into(), ret.into());
-                let store_clone = store.clone();
+                let store_weak = store.weak();
                 unsafe {
 					let trampoline = trampoline::<$($args,)* R>;
                     let (instance, export) = crate::trampoline::generate_raw_func_export(
@@ -1113,11 +1138,10 @@ macro_rules! impl_into_func {
                         ),
                         trampoline,
                         store,
-                        Box::new((self, store_clone)),
+                        Box::new((self, store_weak)),
                     )
                     .expect("failed to generate export");
                     Func {
-                        store: store.clone(),
                         instance,
                         export,
                         trampoline,
diff --git a/crates/api/src/instance.rs b/crates/api/src/instance.rs
index ec883d923e..02c535e773 100644
--- a/crates/api/src/instance.rs
+++ b/crates/api/src/instance.rs
@@ -1,12 +1,9 @@
-use crate::externals::{Export, Extern, Global, Memory, Table};
-use crate::func::Func;
-use crate::module::Module;
-use crate::runtime::{Config, Store};
-use crate::trap::Trap;
+use crate::trampoline::StoreInstanceHandle;
+use crate::{Export, Extern, Func, Global, Memory, Module, Store, Table, Trap};
 use anyhow::{bail, Error, Result};
 use std::any::Any;
 use wasmtime_jit::{CompiledModule, Resolver};
-use wasmtime_runtime::{InstanceHandle, InstantiationError, SignatureRegistry};
+use wasmtime_runtime::{InstantiationError, SignatureRegistry};
 
 struct SimpleResolver<'a> {
     imports: &'a [Extern],
@@ -21,22 +18,35 @@ impl Resolver for SimpleResolver<'_> {
 }
 
 fn instantiate(
-    config: &Config,
+    store: &Store,
     compiled_module: &CompiledModule,
     imports: &[Extern],
     sig_registry: &SignatureRegistry,
     host: Box<dyn Any>,
-) -> Result<InstanceHandle, Error> {
+) -> Result<StoreInstanceHandle, Error> {
     let mut resolver = SimpleResolver { imports };
     unsafe {
-        let instance = compiled_module
-            .instantiate(
+        let config = store.engine().config();
+        let instance = compiled_module.instantiate(
+            &mut resolver,
+            sig_registry,
+            config.memory_creator.as_ref().map(|a| a as _),
+            host,
+        )?;
+
+        // After we've created the `InstanceHandle` we still need to run
+        // initialization to set up data/elements/etc. We do this after adding
+        // the `InstanceHandle` to the store though. This is required for safety
+        // because the start function (for example) may trap, but element
+        // initializers may have run which placed elements into other instance's
+        // tables. This means that from this point on, regardless of whether
+        // initialization is successful, we need to keep the instance alive.
+        let instance = store.add_instance(instance);
+        instance
+            .initialize(
                 config.validating_config.operator_config.enable_bulk_memory,
-                &mut resolver,
-                sig_registry,
-                config.memory_creator.as_ref().map(|a| a as _),
                 config.max_wasm_stack,
-                host,
+                &compiled_module.data_initializers(),
             )
             .map_err(|e| -> Error {
                 match e {
@@ -68,7 +78,7 @@ fn instantiate(
 /// call any code or execute anything!
 #[derive(Clone)]
 pub struct Instance {
-    pub(crate) instance_handle: InstanceHandle,
+    pub(crate) handle: StoreInstanceHandle,
     module: Module,
 }
 
@@ -137,9 +147,8 @@ impl Instance {
         }
 
         let info = module.register_frame_info();
-        let config = store.engine().config();
-        let instance_handle = instantiate(
-            config,
+        let handle = instantiate(
+            store,
             module.compiled_module(),
             imports,
             store.compiler().signatures(),
@@ -147,7 +156,7 @@ impl Instance {
         )?;
 
         Ok(Instance {
-            instance_handle,
+            handle,
             module: module.clone(),
         })
     }
@@ -164,15 +173,11 @@ impl Instance {
     pub fn exports<'instance>(
         &'instance self,
     ) -> impl ExactSizeIterator<Item = Export<'instance>> + 'instance {
-        let instance_handle = &self.instance_handle;
-        let store = self.module.store();
-        self.instance_handle
-            .exports()
-            .map(move |(name, entity_index)| {
-                let export = instance_handle.lookup_by_declaration(entity_index);
-                let extern_ = Extern::from_wasmtime_export(export, store, instance_handle.clone());
-                Export::new(name, extern_)
-            })
+        self.handle.exports().map(move |(name, entity_index)| {
+            let export = self.handle.lookup_by_declaration(entity_index);
+            let extern_ = Extern::from_wasmtime_export(export, self.handle.clone());
+            Export::new(name, extern_)
+        })
     }
 
     /// Looks up an exported [`Extern`] value by name.
@@ -182,12 +187,8 @@ impl Instance {
     ///
     /// Returns `None` if there was no export named `name`.
     pub fn get_export(&self, name: &str) -> Option<Extern> {
-        let export = self.instance_handle.lookup(&name)?;
-        Some(Extern::from_wasmtime_export(
-            export,
-            self.module.store(),
-            self.instance_handle.clone(),
-        ))
+        let export = self.handle.lookup(&name)?;
+        Some(Extern::from_wasmtime_export(export, self.handle.clone()))
     }
 
     /// Looks up an exported [`Func`] value by name.
@@ -221,9 +222,4 @@ impl Instance {
     pub fn get_global(&self, name: &str) -> Option<Global> {
         self.get_export(name)?.into_global()
     }
-
-    #[doc(hidden)]
-    pub fn handle(&self) -> &InstanceHandle {
-        &self.instance_handle
-    }
 }
diff --git a/crates/api/src/runtime.rs b/crates/api/src/runtime.rs
index 716b1324ba..6592cc93df 100644
--- a/crates/api/src/runtime.rs
+++ b/crates/api/src/runtime.rs
@@ -1,18 +1,18 @@
 use crate::externals::MemoryCreator;
-use crate::trampoline::MemoryCreatorProxy;
+use crate::trampoline::{MemoryCreatorProxy, StoreInstanceHandle};
 use anyhow::{bail, Result};
 use std::cell::RefCell;
 use std::cmp::min;
 use std::fmt;
 use std::path::Path;
-use std::rc::Rc;
+use std::rc::{Rc, Weak};
 use std::sync::Arc;
 use wasmparser::{OperatorValidatorConfig, ValidatingParserConfig};
 use wasmtime_environ::settings::{self, Configurable};
 use wasmtime_environ::{CacheConfig, Tunables};
 use wasmtime_jit::{native, CompilationStrategy, Compiler};
 use wasmtime_profiling::{JitDumpAgent, NullProfilerAgent, ProfilingAgent, VTuneAgent};
-use wasmtime_runtime::{debug_builtins, RuntimeMemoryCreator, VMInterrupts};
+use wasmtime_runtime::{debug_builtins, InstanceHandle, RuntimeMemoryCreator, VMInterrupts};
 
 // Runtime Environment
 
@@ -550,13 +550,13 @@ impl Engine {
 /// ocnfiguration (see [`Config`] for more information).
 #[derive(Clone)]
 pub struct Store {
-    // FIXME(#777) should be `Arc` and this type should be thread-safe
     inner: Rc<StoreInner>,
 }
 
-struct StoreInner {
+pub(crate) struct StoreInner {
     engine: Engine,
     compiler: RefCell<Compiler>,
+    instances: RefCell<Vec<InstanceHandle>>,
 }
 
 impl Store {
@@ -573,10 +573,15 @@ impl Store {
             inner: Rc::new(StoreInner {
                 engine: engine.clone(),
                 compiler: RefCell::new(compiler),
+                instances: RefCell::new(Vec::new()),
             }),
         }
     }
 
+    pub(crate) fn from_inner(inner: Rc<StoreInner>) -> Store {
+        Store { inner }
+    }
+
     /// Returns the [`Engine`] that this store is associated with.
     pub fn engine(&self) -> &Engine {
         &self.inner.engine
@@ -595,6 +600,31 @@ impl Store {
         self.inner.compiler.borrow_mut()
     }
 
+    pub(crate) unsafe fn add_instance(&self, handle: InstanceHandle) -> StoreInstanceHandle {
+        self.inner.instances.borrow_mut().push(handle.clone());
+        StoreInstanceHandle {
+            store: self.clone(),
+            handle,
+        }
+    }
+
+    pub(crate) fn existing_instance_handle(&self, handle: InstanceHandle) -> StoreInstanceHandle {
+        debug_assert!(self
+            .inner
+            .instances
+            .borrow()
+            .iter()
+            .any(|i| i.vmctx_ptr() == handle.vmctx_ptr()));
+        StoreInstanceHandle {
+            store: self.clone(),
+            handle,
+        }
+    }
+
+    pub(crate) fn weak(&self) -> Weak<StoreInner> {
+        Rc::downgrade(&self.inner)
+    }
+
     /// Returns whether the stores `a` and `b` refer to the same underlying
     /// `Store`.
     ///
@@ -703,6 +733,16 @@ impl Default for Store {
     }
 }
 
+impl Drop for StoreInner {
+    fn drop(&mut self) {
+        for instance in self.instances.get_mut().iter() {
+            unsafe {
+                instance.dealloc();
+            }
+        }
+    }
+}
+
 /// A threadsafe handle used to interrupt instances executing within a
 /// particular `Store`.
 ///
diff --git a/crates/api/src/trampoline/create_handle.rs b/crates/api/src/trampoline/create_handle.rs
index 3fa2c68410..428c6c35ac 100644
--- a/crates/api/src/trampoline/create_handle.rs
+++ b/crates/api/src/trampoline/create_handle.rs
@@ -1,9 +1,10 @@
 //! Support for a calling of an imported function.
 
-use crate::runtime::Store;
+use crate::trampoline::StoreInstanceHandle;
+use crate::Store;
 use anyhow::Result;
 use std::any::Any;
-use std::collections::{HashMap, HashSet};
+use std::collections::HashMap;
 use std::sync::Arc;
 use wasmtime_environ::entity::PrimaryMap;
 use wasmtime_environ::wasm::DefinedFuncIndex;
@@ -18,15 +19,13 @@ pub(crate) fn create_handle(
     finished_functions: PrimaryMap<DefinedFuncIndex, *mut [VMFunctionBody]>,
     trampolines: HashMap<VMSharedSignatureIndex, VMTrampoline>,
     state: Box<dyn Any>,
-) -> Result<InstanceHandle> {
+) -> Result<StoreInstanceHandle> {
     let imports = Imports::new(
-        HashSet::new(),
         PrimaryMap::new(),
         PrimaryMap::new(),
         PrimaryMap::new(),
         PrimaryMap::new(),
     );
-    let data_initializers = Vec::new();
 
     // Compute indices into the shared signature table.
     let signatures = module
@@ -37,24 +36,17 @@ pub(crate) fn create_handle(
         .collect::<PrimaryMap<_, _>>();
 
     unsafe {
-        Ok(InstanceHandle::new(
+        let handle = InstanceHandle::new(
             Arc::new(module),
             finished_functions.into_boxed_slice(),
             trampolines,
             imports,
             store.memory_creator(),
-            &data_initializers,
             signatures.into_boxed_slice(),
             None,
-            store
-                .engine()
-                .config()
-                .validating_config
-                .operator_config
-                .enable_bulk_memory,
             state,
             store.compiler().interrupts().clone(),
-            store.engine().config().max_wasm_stack,
-        )?)
+        )?;
+        Ok(store.add_instance(handle))
     }
 }
diff --git a/crates/api/src/trampoline/func.rs b/crates/api/src/trampoline/func.rs
index 0c5f36c625..c54f5f0fcb 100644
--- a/crates/api/src/trampoline/func.rs
+++ b/crates/api/src/trampoline/func.rs
@@ -1,6 +1,7 @@
 //! Support for a calling of an imported function.
 
 use super::create_handle::create_handle;
+use crate::trampoline::StoreInstanceHandle;
 use crate::{FuncType, Store, Trap};
 use anyhow::{bail, Result};
 use std::any::Any;
@@ -203,7 +204,7 @@ pub fn create_handle_with_function(
     ft: &FuncType,
     func: Box<dyn Fn(*mut VMContext, *mut u128) -> Result<(), Trap>>,
     store: &Store,
-) -> Result<(InstanceHandle, VMTrampoline)> {
+) -> Result<(StoreInstanceHandle, VMTrampoline)> {
     let isa = {
         let isa_builder = native::builder();
         let flag_builder = settings::builder();
@@ -267,7 +268,7 @@ pub unsafe fn create_handle_with_raw_function(
     trampoline: VMTrampoline,
     store: &Store,
     state: Box<dyn Any>,
-) -> Result<InstanceHandle> {
+) -> Result<StoreInstanceHandle> {
     let isa = {
         let isa_builder = native::builder();
         let flag_builder = settings::builder();
diff --git a/crates/api/src/trampoline/global.rs b/crates/api/src/trampoline/global.rs
index db2366fc92..4fa13e42bd 100644
--- a/crates/api/src/trampoline/global.rs
+++ b/crates/api/src/trampoline/global.rs
@@ -1,12 +1,12 @@
 use super::create_handle::create_handle;
+use crate::trampoline::StoreInstanceHandle;
 use crate::Store;
 use crate::{GlobalType, Mutability, Val};
 use anyhow::{bail, Result};
 use wasmtime_environ::entity::PrimaryMap;
 use wasmtime_environ::{wasm, EntityIndex, Module};
-use wasmtime_runtime::InstanceHandle;
 
-pub fn create_global(store: &Store, gt: &GlobalType, val: Val) -> Result<InstanceHandle> {
+pub fn create_global(store: &Store, gt: &GlobalType, val: Val) -> Result<StoreInstanceHandle> {
     let global = wasm::Global {
         ty: match gt.content().get_wasmtime_type() {
             Some(t) => t,
diff --git a/crates/api/src/trampoline/memory.rs b/crates/api/src/trampoline/memory.rs
index b3a2bf6a46..a5fe8f6ffd 100644
--- a/crates/api/src/trampoline/memory.rs
+++ b/crates/api/src/trampoline/memory.rs
@@ -1,17 +1,19 @@
 use super::create_handle::create_handle;
 use crate::externals::{LinearMemory, MemoryCreator};
+use crate::trampoline::StoreInstanceHandle;
 use crate::Store;
 use crate::{Limits, MemoryType};
 use anyhow::Result;
 use wasmtime_environ::entity::PrimaryMap;
 use wasmtime_environ::{wasm, EntityIndex, MemoryPlan, Module, WASM_PAGE_SIZE};
-use wasmtime_runtime::{
-    InstanceHandle, RuntimeLinearMemory, RuntimeMemoryCreator, VMMemoryDefinition,
-};
+use wasmtime_runtime::{RuntimeLinearMemory, RuntimeMemoryCreator, VMMemoryDefinition};
 
 use std::sync::Arc;
 
-pub fn create_handle_with_memory(store: &Store, memory: &MemoryType) -> Result<InstanceHandle> {
+pub fn create_handle_with_memory(
+    store: &Store,
+    memory: &MemoryType,
+) -> Result<StoreInstanceHandle> {
     let mut module = Module::new();
 
     let memory = wasm::Memory {
diff --git a/crates/api/src/trampoline/mod.rs b/crates/api/src/trampoline/mod.rs
index 563924e413..a3a6aac71a 100644
--- a/crates/api/src/trampoline/mod.rs
+++ b/crates/api/src/trampoline/mod.rs
@@ -15,14 +15,42 @@ use self::table::create_handle_with_table;
 use crate::{FuncType, GlobalType, MemoryType, Store, TableType, Trap, Val};
 use anyhow::Result;
 use std::any::Any;
-use wasmtime_runtime::{VMContext, VMFunctionBody, VMTrampoline};
+use std::ops::Deref;
+use wasmtime_runtime::{InstanceHandle, VMContext, VMFunctionBody, VMTrampoline};
+
+/// A wrapper around `wasmtime_runtime::InstanceHandle` which pairs it with the
+/// `Store` that it's rooted within. The instance is deallocated when `Store` is
+/// deallocated, so this is a safe handle in terms of memory management for the
+/// `Store`.
+pub struct StoreInstanceHandle {
+    pub store: Store,
+    pub handle: InstanceHandle,
+}
+
+impl Clone for StoreInstanceHandle {
+    fn clone(&self) -> StoreInstanceHandle {
+        StoreInstanceHandle {
+            store: self.store.clone(),
+            // Note should be safe because the lifetime of the instance handle
+            // is tied to the `Store` which this is paired with.
+            handle: unsafe { self.handle.clone() },
+        }
+    }
+}
+
+impl Deref for StoreInstanceHandle {
+    type Target = InstanceHandle;
+    fn deref(&self) -> &InstanceHandle {
+        &self.handle
+    }
+}
 
 pub fn generate_func_export(
     ft: &FuncType,
     func: Box<dyn Fn(*mut VMContext, *mut u128) -> Result<(), Trap>>,
     store: &Store,
 ) -> Result<(
-    wasmtime_runtime::InstanceHandle,
+    StoreInstanceHandle,
     wasmtime_runtime::ExportFunction,
     VMTrampoline,
 )> {
@@ -42,10 +70,7 @@ pub unsafe fn generate_raw_func_export(
     trampoline: VMTrampoline,
     store: &Store,
     state: Box<dyn Any>,
-) -> Result<(
-    wasmtime_runtime::InstanceHandle,
-    wasmtime_runtime::ExportFunction,
-)> {
+) -> Result<(StoreInstanceHandle, wasmtime_runtime::ExportFunction)> {
     let instance = func::create_handle_with_raw_function(ft, func, trampoline, store, state)?;
     match instance.lookup("trampoline").expect("trampoline export") {
         wasmtime_runtime::Export::Function(f) => Ok((instance, f)),
@@ -57,10 +82,7 @@ pub fn generate_global_export(
     store: &Store,
     gt: &GlobalType,
     val: Val,
-) -> Result<(
-    wasmtime_runtime::InstanceHandle,
-    wasmtime_runtime::ExportGlobal,
-)> {
+) -> Result<(StoreInstanceHandle, wasmtime_runtime::ExportGlobal)> {
     let instance = create_global(store, gt, val)?;
     match instance.lookup("global").expect("global export") {
         wasmtime_runtime::Export::Global(g) => Ok((instance, g)),
@@ -71,10 +93,7 @@ pub fn generate_global_export(
 pub fn generate_memory_export(
     store: &Store,
     m: &MemoryType,
-) -> Result<(
-    wasmtime_runtime::InstanceHandle,
-    wasmtime_runtime::ExportMemory,
-)> {
+) -> Result<(StoreInstanceHandle, wasmtime_runtime::ExportMemory)> {
     let instance = create_handle_with_memory(store, m)?;
     match instance.lookup("memory").expect("memory export") {
         wasmtime_runtime::Export::Memory(m) => Ok((instance, m)),
@@ -85,10 +104,7 @@ pub fn generate_memory_export(
 pub fn generate_table_export(
     store: &Store,
     t: &TableType,
-) -> Result<(
-    wasmtime_runtime::InstanceHandle,
-    wasmtime_runtime::ExportTable,
-)> {
+) -> Result<(StoreInstanceHandle, wasmtime_runtime::ExportTable)> {
     let instance = create_handle_with_table(store, t)?;
     match instance.lookup("table").expect("table export") {
         wasmtime_runtime::Export::Table(t) => Ok((instance, t)),
diff --git a/crates/api/src/trampoline/table.rs b/crates/api/src/trampoline/table.rs
index eb6c12dd65..4919e0e09c 100644
--- a/crates/api/src/trampoline/table.rs
+++ b/crates/api/src/trampoline/table.rs
@@ -1,12 +1,12 @@
 use super::create_handle::create_handle;
+use crate::trampoline::StoreInstanceHandle;
 use crate::Store;
 use crate::{TableType, ValType};
 use anyhow::{bail, Result};
 use wasmtime_environ::entity::PrimaryMap;
 use wasmtime_environ::{wasm, EntityIndex, Module};
-use wasmtime_runtime::InstanceHandle;
 
-pub fn create_handle_with_table(store: &Store, table: &TableType) -> Result<InstanceHandle> {
+pub fn create_handle_with_table(store: &Store, table: &TableType) -> Result<StoreInstanceHandle> {
     let mut module = Module::new();
 
     let table = wasm::Table {
diff --git a/crates/api/src/unix.rs b/crates/api/src/unix.rs
index f17eecfe13..22fa392597 100644
--- a/crates/api/src/unix.rs
+++ b/crates/api/src/unix.rs
@@ -26,6 +26,6 @@ impl InstanceExt for Instance {
     where
         H: 'static + Fn(libc::c_int, *const libc::siginfo_t, *const libc::c_void) -> bool,
     {
-        self.instance_handle.clone().set_signal_handler(handler);
+        self.handle.set_signal_handler(handler);
     }
 }
diff --git a/crates/api/src/values.rs b/crates/api/src/values.rs
index a9387a7338..8d1d7f55be 100644
--- a/crates/api/src/values.rs
+++ b/crates/api/src/values.rs
@@ -224,6 +224,7 @@ pub(crate) fn from_checked_anyfunc(
         signature: item.type_index,
         vmctx: item.vmctx,
     };
-    let f = Func::from_wasmtime_function(export, store, instance_handle);
+    let instance = store.existing_instance_handle(instance_handle);
+    let f = Func::from_wasmtime_function(export, instance);
     Val::FuncRef(f)
 }
diff --git a/crates/api/src/windows.rs b/crates/api/src/windows.rs
index 962cae7458..5725007d53 100644
--- a/crates/api/src/windows.rs
+++ b/crates/api/src/windows.rs
@@ -26,6 +26,6 @@ impl InstanceExt for Instance {
     where
         H: 'static + Fn(winapi::um::winnt::PEXCEPTION_POINTERS) -> bool,
     {
-        self.instance_handle.clone().set_signal_handler(handler);
+        self.handle.set_signal_handler(handler);
     }
 }
diff --git a/crates/jit/src/imports.rs b/crates/jit/src/imports.rs
index 743b6e512e..d2ef3536fc 100644
--- a/crates/jit/src/imports.rs
+++ b/crates/jit/src/imports.rs
@@ -2,14 +2,13 @@
 
 use crate::resolver::Resolver;
 use more_asserts::assert_ge;
-use std::collections::HashSet;
 use std::convert::TryInto;
 use wasmtime_environ::entity::PrimaryMap;
 use wasmtime_environ::wasm::{Global, GlobalInit, Memory, Table, TableElementType};
 use wasmtime_environ::{EntityIndex, MemoryPlan, MemoryStyle, Module, TablePlan};
 use wasmtime_runtime::{
-    Export, Imports, InstanceHandle, LinkError, SignatureRegistry, VMFunctionImport,
-    VMGlobalImport, VMMemoryImport, VMTableImport,
+    Export, Imports, LinkError, SignatureRegistry, VMFunctionImport, VMGlobalImport,
+    VMMemoryImport, VMTableImport,
 };
 
 /// This function allows to match all imports of a `Module` with concrete definitions provided by
@@ -21,8 +20,6 @@ pub fn resolve_imports(
     signatures: &SignatureRegistry,
     resolver: &mut dyn Resolver,
 ) -> Result<Imports, LinkError> {
-    let mut dependencies = HashSet::new();
-
     let mut function_imports = PrimaryMap::with_capacity(module.local.num_imported_funcs);
     let mut table_imports = PrimaryMap::with_capacity(module.local.num_imported_tables);
     let mut memory_imports = PrimaryMap::with_capacity(module.local.num_imported_memories);
@@ -45,7 +42,6 @@ pub fn resolve_imports(
                         module_name, field_name, signature, import_signature
                     )));
                 }
-                dependencies.insert(unsafe { InstanceHandle::from_vmctx(f.vmctx) });
                 function_imports.push(VMFunctionImport {
                     body: f.address,
                     vmctx: f.vmctx,
@@ -73,7 +69,6 @@ pub fn resolve_imports(
                         module_name, field_name,
                     )));
                 }
-                dependencies.insert(unsafe { InstanceHandle::from_vmctx(t.vmctx) });
                 table_imports.push(VMTableImport {
                     from: t.definition,
                     vmctx: t.vmctx,
@@ -115,7 +110,6 @@ pub fn resolve_imports(
                 }
                 assert_ge!(m.memory.offset_guard_size, import_memory.offset_guard_size);
 
-                dependencies.insert(unsafe { InstanceHandle::from_vmctx(m.vmctx) });
                 memory_imports.push(VMMemoryImport {
                     from: m.definition,
                     vmctx: m.vmctx,
@@ -143,7 +137,6 @@ pub fn resolve_imports(
                         module_name, field_name
                     )));
                 }
-                dependencies.insert(unsafe { InstanceHandle::from_vmctx(g.vmctx) });
                 global_imports.push(VMGlobalImport { from: g.definition });
             }
             (EntityIndex::Global(_), Some(_)) => {
@@ -162,7 +155,6 @@ pub fn resolve_imports(
     }
 
     Ok(Imports::new(
-        dependencies,
         function_imports,
         table_imports,
         memory_imports,
diff --git a/crates/jit/src/instantiate.rs b/crates/jit/src/instantiate.rs
index c7bcb73df6..e3f1a5eb96 100644
--- a/crates/jit/src/instantiate.rs
+++ b/crates/jit/src/instantiate.rs
@@ -204,21 +204,11 @@ impl CompiledModule {
     /// See `InstanceHandle::new`
     pub unsafe fn instantiate(
         &self,
-        is_bulk_memory: bool,
         resolver: &mut dyn Resolver,
         sig_registry: &SignatureRegistry,
         mem_creator: Option<&dyn RuntimeMemoryCreator>,
-        max_wasm_stack: usize,
         host_state: Box<dyn Any>,
     ) -> Result<InstanceHandle, InstantiationError> {
-        let data_initializers = self
-            .data_initializers
-            .iter()
-            .map(|init| DataInitializer {
-                location: init.location.clone(),
-                data: &*init.data,
-            })
-            .collect::<Vec<_>>();
         let imports = resolve_imports(&self.module, &sig_registry, resolver)?;
         InstanceHandle::new(
             Arc::clone(&self.module),
@@ -226,16 +216,24 @@ impl CompiledModule {
             self.trampolines.clone(),
             imports,
             mem_creator,
-            &data_initializers,
             self.signatures.clone(),
             self.dbg_jit_registration.as_ref().map(|r| Rc::clone(&r)),
-            is_bulk_memory,
             host_state,
             self.interrupts.clone(),
-            max_wasm_stack,
         )
     }
 
+    /// Returns data initializers to pass to `InstanceHandle::initialize`
+    pub fn data_initializers(&self) -> Vec<DataInitializer<'_>> {
+        self.data_initializers
+            .iter()
+            .map(|init| DataInitializer {
+                location: init.location.clone(),
+                data: &*init.data,
+            })
+            .collect()
+    }
+
     /// Return a reference-counting pointer to a module.
     pub fn module(&self) -> &Arc<Module> {
         &self.module
diff --git a/crates/runtime/src/imports.rs b/crates/runtime/src/imports.rs
index 0214ce67b0..14360a7036 100644
--- a/crates/runtime/src/imports.rs
+++ b/crates/runtime/src/imports.rs
@@ -1,15 +1,10 @@
-use crate::instance::InstanceHandle;
 use crate::vmcontext::{VMFunctionImport, VMGlobalImport, VMMemoryImport, VMTableImport};
-use std::collections::HashSet;
 use wasmtime_environ::entity::{BoxedSlice, PrimaryMap};
 use wasmtime_environ::wasm::{FuncIndex, GlobalIndex, MemoryIndex, TableIndex};
 
 /// Resolved import pointers.
 #[derive(Clone)]
 pub struct Imports {
-    /// The set of instances that the imports depend on.
-    pub dependencies: HashSet<InstanceHandle>,
-
     /// Resolved addresses for imported functions.
     pub functions: BoxedSlice<FuncIndex, VMFunctionImport>,
 
@@ -26,14 +21,12 @@ pub struct Imports {
 impl Imports {
     /// Construct a new `Imports` instance.
     pub fn new(
-        dependencies: HashSet<InstanceHandle>,
         function_imports: PrimaryMap<FuncIndex, VMFunctionImport>,
         table_imports: PrimaryMap<TableIndex, VMTableImport>,
         memory_imports: PrimaryMap<MemoryIndex, VMMemoryImport>,
         global_imports: PrimaryMap<GlobalIndex, VMGlobalImport>,
     ) -> Self {
         Self {
-            dependencies,
             functions: function_imports.into_boxed_slice(),
             tables: table_imports.into_boxed_slice(),
             memories: memory_imports.into_boxed_slice(),
@@ -44,7 +37,6 @@ impl Imports {
     /// Construct a new `Imports` instance with no imports.
     pub fn none() -> Self {
         Self {
-            dependencies: HashSet::new(),
             functions: PrimaryMap::new().into_boxed_slice(),
             tables: PrimaryMap::new().into_boxed_slice(),
             memories: PrimaryMap::new().into_boxed_slice(),
diff --git a/crates/runtime/src/instance.rs b/crates/runtime/src/instance.rs
index ef5e176600..bbf4ebfaba 100644
--- a/crates/runtime/src/instance.rs
+++ b/crates/runtime/src/instance.rs
@@ -20,7 +20,7 @@ use more_asserts::assert_lt;
 use std::alloc::{self, Layout};
 use std::any::Any;
 use std::cell::{Cell, RefCell};
-use std::collections::{HashMap, HashSet};
+use std::collections::HashMap;
 use std::convert::TryFrom;
 use std::rc::Rc;
 use std::sync::Arc;
@@ -39,7 +39,7 @@ cfg_if::cfg_if! {
 
         impl InstanceHandle {
             /// Set a custom signal handler
-            pub fn set_signal_handler<H>(&mut self, handler: H)
+            pub fn set_signal_handler<H>(&self, handler: H)
             where
                 H: 'static + Fn(libc::c_int, *const libc::siginfo_t, *const libc::c_void) -> bool,
             {
@@ -51,7 +51,7 @@ cfg_if::cfg_if! {
 
         impl InstanceHandle {
             /// Set a custom signal handler
-            pub fn set_signal_handler<H>(&mut self, handler: H)
+            pub fn set_signal_handler<H>(&self, handler: H)
             where
                 H: 'static + Fn(winapi::um::winnt::PEXCEPTION_POINTERS) -> bool,
             {
@@ -66,14 +66,6 @@ cfg_if::cfg_if! {
 /// This is repr(C) to ensure that the vmctx field is last.
 #[repr(C)]
 pub(crate) struct Instance {
-    /// The number of references to this `Instance`.
-    refcount: Cell<usize>,
-
-    /// `Instance`s from which this `Instance` imports. These won't
-    /// create reference cycles because wasm instances can't cyclically
-    /// import from each other.
-    dependencies: HashSet<InstanceHandle>,
-
     /// The `Module` this `Instance` was instantiated from.
     module: Arc<Module>,
 
@@ -878,13 +870,10 @@ impl InstanceHandle {
         trampolines: HashMap<VMSharedSignatureIndex, VMTrampoline>,
         imports: Imports,
         mem_creator: Option<&dyn RuntimeMemoryCreator>,
-        data_initializers: &[DataInitializer<'_>],
         vmshared_signatures: BoxedSlice<SignatureIndex, VMSharedSignatureIndex>,
         dbg_jit_registration: Option<Rc<GdbJitImageRegistration>>,
-        is_bulk_memory: bool,
         host_state: Box<dyn Any>,
         interrupts: Arc<VMInterrupts>,
-        max_wasm_stack: usize,
     ) -> Result<Self, InstantiationError> {
         let tables = create_tables(&module);
         let memories = create_memories(&module, mem_creator.unwrap_or(&DefaultMemoryCreator {}))?;
@@ -909,8 +898,6 @@ impl InstanceHandle {
 
         let handle = {
             let instance = Instance {
-                refcount: Cell::new(1),
-                dependencies: imports.dependencies,
                 module,
                 offsets,
                 memories,
@@ -983,30 +970,44 @@ impl InstanceHandle {
         );
         *instance.interrupts() = &*instance.interrupts;
 
+        // Ensure that our signal handlers are ready for action.
+        // TODO: Move these calls out of `InstanceHandle`.
+        traphandlers::init();
+
+        // Perform infallible initialization in this constructor, while fallible
+        // initialization is deferred to the `initialize` method.
+        initialize_passive_elements(instance);
+        initialize_globals(instance);
+
+        Ok(handle)
+    }
+
+    /// Finishes the instantiation process started by `Instance::new`.
+    ///
+    /// Only safe to call immediately after instantiation.
+    pub unsafe fn initialize(
+        &self,
+        is_bulk_memory: bool,
+        max_wasm_stack: usize,
+        data_initializers: &[DataInitializer<'_>],
+    ) -> Result<(), InstantiationError> {
         // Check initializer bounds before initializing anything. Only do this
         // when bulk memory is disabled, since the bulk memory proposal changes
         // instantiation such that the intermediate results of failed
         // initializations are visible.
         if !is_bulk_memory {
-            check_table_init_bounds(instance)?;
-            check_memory_init_bounds(instance, data_initializers)?;
+            check_table_init_bounds(self.instance())?;
+            check_memory_init_bounds(self.instance(), data_initializers)?;
         }
 
-        // Apply the initializers.
-        initialize_tables(instance)?;
-        initialize_passive_elements(instance);
-        initialize_memories(instance, data_initializers)?;
-        initialize_globals(instance);
+        // Apply fallible initializers. Note that this can "leak" state even if
+        // it fails.
+        initialize_tables(self.instance())?;
+        initialize_memories(self.instance(), data_initializers)?;
 
-        // Ensure that our signal handlers are ready for action.
-        // TODO: Move these calls out of `InstanceHandle`.
-        traphandlers::init();
-
-        // The WebAssembly spec specifies that the start function is
-        // invoked automatically at instantiation time.
-        instance.invoke_start_function(max_wasm_stack)?;
-
-        Ok(handle)
+        // And finally, invoke the start function.
+        self.instance().invoke_start_function(max_wasm_stack)?;
+        Ok(())
     }
 
     /// Create a new `InstanceHandle` pointing at the instance
@@ -1017,7 +1018,6 @@ impl InstanceHandle {
     /// be a `VMContext` allocated as part of an `Instance`.
     pub unsafe fn from_vmctx(vmctx: *mut VMContext) -> Self {
         let instance = (&mut *vmctx).instance();
-        instance.refcount.set(instance.refcount.get() + 1);
         Self {
             instance: instance as *const Instance as *mut Instance,
         }
@@ -1130,30 +1130,29 @@ impl InstanceHandle {
     pub(crate) fn instance(&self) -> &Instance {
         unsafe { &*(self.instance as *const Instance) }
     }
-}
 
-impl Clone for InstanceHandle {
-    fn clone(&self) -> Self {
-        let instance = self.instance();
-        instance.refcount.set(instance.refcount.get() + 1);
-        Self {
+    /// Returns a clone of this instance.
+    ///
+    /// This is unsafe because the returned handle here is just a cheap clone
+    /// of the internals, there's no lifetime tracking around its validity.
+    /// You'll need to ensure that the returned handles all go out of scope at
+    /// the same time.
+    pub unsafe fn clone(&self) -> InstanceHandle {
+        InstanceHandle {
             instance: self.instance,
         }
     }
-}
 
-impl Drop for InstanceHandle {
-    fn drop(&mut self) {
+    /// Deallocates memory associated with this instance.
+    ///
+    /// Note that this is unsafe because there might be other handles to this
+    /// `InstanceHandle` elsewhere, and there's nothing preventing usage of
+    /// this handle after this function is called.
+    pub unsafe fn dealloc(&self) {
         let instance = self.instance();
-        let count = instance.refcount.get();
-        instance.refcount.set(count - 1);
-        if count == 1 {
-            let layout = instance.alloc_layout();
-            unsafe {
-                ptr::drop_in_place(self.instance);
-                alloc::dealloc(self.instance.cast(), layout);
-            }
-        }
+        let layout = instance.alloc_layout();
+        ptr::drop_in_place(self.instance);
+        alloc::dealloc(self.instance.cast(), layout);
     }
 }
 
diff --git a/tests/all/func.rs b/tests/all/func.rs
index 40616810ed..ea55840564 100644
--- a/tests/all/func.rs
+++ b/tests/all/func.rs
@@ -39,6 +39,7 @@ fn dtor_runs() {
     Func::wrap(&store, move || {
         drop(&a);
     });
+    drop(store);
     assert_eq!(HITS.load(SeqCst), 1);
 }
 
@@ -63,7 +64,7 @@ fn dtor_delayed() -> Result<()> {
     let module = Module::new(&store, &wasm)?;
     let instance = Instance::new(&module, &[func.into()])?;
     assert_eq!(HITS.load(SeqCst), 0);
-    drop(instance);
+    drop((instance, module, store));
     assert_eq!(HITS.load(SeqCst), 1);
     Ok(())
 }
diff --git a/tests/all/main.rs b/tests/all/main.rs
index 2f819c1a54..95b7d6ba44 100644
--- a/tests/all/main.rs
+++ b/tests/all/main.rs
@@ -15,4 +15,5 @@ mod memory_creator;
 mod name;
 mod stack_overflow;
 mod traps;
+mod use_after_drop;
 mod wast;
diff --git a/tests/all/memory_creator.rs b/tests/all/memory_creator.rs
index ed80cc72c9..b53dcd2c82 100644
--- a/tests/all/memory_creator.rs
+++ b/tests/all/memory_creator.rs
@@ -175,9 +175,9 @@ mod not_for_windows {
         let tot_pages = *mem_creator.num_total_pages.lock().unwrap();
         assert_eq!(tot_pages, 4);
 
-        drop(instance1);
+        drop((instance1, instance2, store, module));
         let tot_pages = *mem_creator.num_total_pages.lock().unwrap();
-        assert_eq!(tot_pages, 2);
+        assert_eq!(tot_pages, 0);
 
         Ok(())
     }
diff --git a/tests/all/use_after_drop.rs b/tests/all/use_after_drop.rs
new file mode 100644
index 0000000000..b1f45041ce
--- /dev/null
+++ b/tests/all/use_after_drop.rs
@@ -0,0 +1,21 @@
+use anyhow::Result;
+use wasmtime::*;
+
+#[test]
+fn use_func_after_drop() -> Result<()> {
+    let table;
+    {
+        let store = Store::default();
+        let closed_over_data = String::from("abcd");
+        let func = Func::wrap(&store, move || {
+            assert_eq!(closed_over_data, "abcd");
+        });
+        let ty = TableType::new(ValType::FuncRef, Limits::new(1, None));
+        table = Table::new(&store, ty, Val::AnyRef(AnyRef::Null))?;
+        table.set(0, func.into())?;
+    }
+    let func = table.get(0).unwrap().funcref().unwrap().clone();
+    let func = func.get0::<()>()?;
+    func()?;
+    Ok(())
+}