diff --git a/rs/private/crate_git_repository.bzl b/rs/private/crate_git_repository.bzl
--- a/rs/private/crate_git_repository.bzl
+++ b/rs/private/crate_git_repository.bzl
@@ -35,6 +35,14 @@
         "HEAD"
     ])
     if result.return_code != 0:
         fail(result.stderr)

+    # Remove .git worktree pointer file. It contains an absolute path to
+    # the bazel output base which is machine-specific and non-deterministic.
+    # Leaving it in pollutes compile_data globs and causes AC misses.
+    #
+    # Note that bazelbuild/rules_rust ignores .git (among other paths) during splicing:
+    # https://github.com/bazelbuild/rules_rust/blob/ca4915c0210bcd240152a5333ecb24d266bda144/crate_universe/src/splicing/splicer.rs#L42
+    rctx.delete(root.get_child(".git"))
+
     if strip_prefix:
         dest_link = dest_dir.get_child(strip_prefix)
         if not dest_link.exists: