diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b880bfafb3..530f8941fa 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -400,7 +400,7 @@ jobs:
         submodules: true
     - name: Install Rust
       run: rustup update stable && rustup default stable
-    - run: cd cranelift/codegen && cargo build --features all-arch
+    - run: cd cranelift/codegen && cargo build --features "all-arch completely-skip-isle-for-ci-deterministic-check"
     - run: ci/ensure_deterministic_build.sh
 
   # Perform release builds of `wasmtime` and `libwasmtime.so`. Builds on
diff --git a/cranelift/codegen/Cargo.toml b/cranelift/codegen/Cargo.toml
index ae8066ac16..ba7e7488b6 100644
--- a/cranelift/codegen/Cargo.toml
+++ b/cranelift/codegen/Cargo.toml
@@ -104,6 +104,10 @@ souper-harvest = ["souper-ir", "souper-ir/stringify"]
 # Recompile ISLE DSL source files into their generated Rust code.
 rebuild-isle = ["isle", "cranelift-codegen-meta/rebuild-isle"]
 
+# A hack to skip the ISLE-rebuild logic when testing for determinism
+# with the "Meta deterministic check" CI job.
+completely-skip-isle-for-ci-deterministic-check = []
+
 [badges]
 maintenance = { status = "experimental" }
 
diff --git a/cranelift/codegen/build.rs b/cranelift/codegen/build.rs
index a3f31c7db9..adb99386c5 100644
--- a/cranelift/codegen/build.rs
+++ b/cranelift/codegen/build.rs
@@ -78,7 +78,17 @@ fn main() {
         .unwrap()
     }
 
-    maybe_rebuild_isle(crate_dir).expect("Unhandled failure in ISLE rebuild");
+    // The "Meta deterministic check" CI job runs this build script N
+    // times to ensure it produces the same output
+    // consistently. However, it runs the script in a fresh directory,
+    // without any of the source tree present; this breaks our
+    // manifest check (we need the ISLE source to be present). To keep
+    // things simple, we just disable all ISLE-related logic for this
+    // specific CI job.
+    #[cfg(not(feature = "completely-skip-isle-for-ci-deterministic-check"))]
+    {
+        maybe_rebuild_isle(crate_dir).expect("Unhandled failure in ISLE rebuild");
+    }
 
     let pkg_version = env::var("CARGO_PKG_VERSION").unwrap();
     let mut cmd = std::process::Command::new("git");
@@ -259,6 +269,9 @@ fn maybe_rebuild_isle(
         }
 
         let manifest = std::fs::read_to_string(compilation.manifest_filename())?;
+        // Canonicalize Windows line-endings into Unix line-endings in
+        // the manifest text itself.
+        let manifest = manifest.replace("\r\n", "\n");
         let expected_manifest = compilation.compute_manifest()?;
         if manifest != expected_manifest {
             rebuild_compilations.push((compilation, expected_manifest));