diff --git a/crates/fuzzing/src/generators/config.rs b/crates/fuzzing/src/generators/config.rs
index aaf435c013..c3016fa6c1 100644
--- a/crates/fuzzing/src/generators/config.rs
+++ b/crates/fuzzing/src/generators/config.rs
@@ -141,6 +141,7 @@ impl Config {
     }
 
     /// Converts this to a `wasmtime::Config` object
+    #[allow(deprecated)] // Allow use of `cranelift_use_egraphs` below.
     pub fn to_wasmtime(&self) -> wasmtime::Config {
         crate::init_fuzzing();
         log::debug!("creating wasmtime config with {:#?}", self.wasmtime);
diff --git a/crates/wasmtime/src/config.rs b/crates/wasmtime/src/config.rs
index 7e42afbc40..88622bc312 100644
--- a/crates/wasmtime/src/config.rs
+++ b/crates/wasmtime/src/config.rs
@@ -841,6 +841,10 @@ impl Config {
     /// The default value for this is `true`.
     #[cfg(compiler)]
     #[cfg_attr(nightlydoc, doc(cfg(feature = "cranelift")))] // see build.rs
+    #[deprecated(
+        since = "5.0.0",
+        note = "egraphs will be the default and this method will be removed in a future version."
+    )]
     pub fn cranelift_use_egraphs(&mut self, enable: bool) -> &mut Self {
         let val = if enable { "true" } else { "false" };
         self.compiler_config