diff --git a/cargo/private/cargo_build_script_runner/bin.rs b/cargo/private/cargo_build_script_runner/bin.rs
index d1fe235b15..210d5d90af 100644
--- a/cargo/private/cargo_build_script_runner/bin.rs
+++ b/cargo/private/cargo_build_script_runner/bin.rs
@@ -113,10 +113,12 @@ fn run_buildrs() -> Result<(), String> {
                 .ok_or_else(|| "Failed while getting file name".to_string())?;
             let link = manifest_dir.join(file_name);
 
-            symlink_if_not_exists(&path, &link)
-                .map_err(|err| format!("Failed to symlink {path:?} to {link:?}: {err}"))?;
-
-            exec_root_links.push(link)
+            // An entry that already exists belongs to CARGO_MANIFEST_DIR and must not be cleaned.
+            if symlink_if_not_exists(&path, &link)
+                .map_err(|err| format!("Failed to symlink {path:?} to {link:?}: {err}"))?
+            {
+                exec_root_links.push(link)
+            }
         }
     }
 
@@ -383,10 +385,14 @@ fn set_script_runfiles_env(script_path: &Path, command: &mut Command) {
 }
 
 /// Create a symlink from `link` to `original` if `link` doesn't already exist.
-fn symlink_if_not_exists(original: &Path, link: &Path) -> Result<(), String> {
-    symlink(original, link)
-        .or_else(swallow_already_exists)
-        .map_err(|err| format!("Failed to create symlink: {err}"))
+///
+/// Returns whether the symlink was created.
+fn symlink_if_not_exists(original: &Path, link: &Path) -> Result<bool, String> {
+    match symlink(original, link) {
+        Ok(()) => Ok(true),
+        Err(err) if err.kind() == std::io::ErrorKind::AlreadyExists => Ok(false),
+        Err(err) => Err(format!("Failed to create symlink: {err}")),
+    }
 }
 
 fn resolve_rundir(rundir: &str, exec_root: &Path, manifest_dir: &Path) -> Result<PathBuf, String> {
@@ -406,14 +412,6 @@ fn resolve_rundir(rundir: &str, exec_root: &Path, manifest_dir: &Path) -> Result
     Ok(exec_root.join(rundir_path))
 }
 
-fn swallow_already_exists(err: std::io::Error) -> std::io::Result<()> {
-    if err.kind() == std::io::ErrorKind::AlreadyExists {
-        Ok(())
-    } else {
-        Err(err)
-    }
-}
-
 /// A representation of expected command line arguments.
 struct Args {
     progname: String,
diff --git a/cargo/tests/cargo_build_script/symlink_exec_root/BUILD.bazel b/cargo/tests/cargo_build_script/symlink_exec_root/BUILD.bazel
index 75f2407dd7..1b01af60fc 100644
--- a/cargo/tests/cargo_build_script/symlink_exec_root/BUILD.bazel
+++ b/cargo/tests/cargo_build_script/symlink_exec_root/BUILD.bazel
@@ -37,21 +37,63 @@ cargo_build_script(
 
 # This is an empty test file, it is only needed to trigger the build script.
 write_file(
-    name = "test_exec_root_access_rs",
-    out = "test_exec_root_access.rs",
+    name = "empty",
+    out = "empty.rs",
     content = [""],
 )
 
 rust_test(
     name = "test_exec_root_access_feature_enabled",
-    srcs = ["test_exec_root_access.rs"],
+    srcs = ["empty.rs"],
     edition = "2021",
     deps = [":test_exec_root_access.build.feature_enabled"],
 )
 
 rust_test(
     name = "test_exec_root_access_feature_disabled",
-    srcs = ["test_exec_root_access.rs"],
+    srcs = ["empty.rs"],
     edition = "2021",
     deps = [":test_exec_root_access.build.feature_disabled"],
 )
+
+###############################################################################
+# Test that a CARGO_MANIFEST_DIR entry which collides with an exec root entry
+# survives the run.
+#
+# The data file below puts a real `external` directory in CARGO_MANIFEST_DIR,
+# and `external` is always a top-level exec root entry, so the runner cannot
+# symlink it. It must then leave that directory alone rather than deleting it
+# along with the symlinks it did create.
+###############################################################################
+
+write_file(
+    name = "exec_root_collision_file",
+    out = "external/exec_root_collision.txt",
+    content = ["This file makes 'external' a real directory in CARGO_MANIFEST_DIR."],
+)
+
+symlink_execroot_cargo_build_script(
+    name = "test_exec_root_collision.build.feature_enabled",
+    script = ":test_exec_root_collision.build.feature_disabled",
+    target_compatible_with = select({
+        "@platforms//os:windows": ["@platforms//:incompatible"],
+        "//conditions:default": [],
+    }),
+)
+
+cargo_build_script(
+    name = "test_exec_root_collision.build.feature_disabled",
+    srcs = ["test_exec_root_collision.build.rs"],
+    crate_name = "test_exec_root_collision",
+    data = [
+        ":exec_root_collision_file",
+    ],
+    edition = "2021",
+)
+
+rust_test(
+    name = "test_exec_root_collision_feature_enabled",
+    srcs = ["empty.rs"],
+    edition = "2021",
+    deps = [":test_exec_root_collision.build.feature_enabled"],
+)
diff --git a/cargo/tests/cargo_build_script/symlink_exec_root/test_exec_root_collision.build.rs b/cargo/tests/cargo_build_script/symlink_exec_root/test_exec_root_collision.build.rs
new file mode 100644
index 0000000000..0dca2e836e
--- /dev/null
+++ b/cargo/tests/cargo_build_script/symlink_exec_root/test_exec_root_collision.build.rs
@@ -0,0 +1,16 @@
+//! A Cargo build script binary used in unit tests for the Bazel `cargo_build_script` rule
+
+fn main() {
+    // `external` is a top-level exec root entry, so the runner will try to symlink it into
+    // CARGO_MANIFEST_DIR, where this data file has already created a real directory of the
+    // same name. The pre-existing directory must win, and must still be readable.
+    let collision = std::path::Path::new("external/exec_root_collision.txt");
+    assert!(
+        collision.is_file(),
+        "'external/exec_root_collision.txt' must be readable from CARGO_MANIFEST_DIR"
+    );
+    assert_eq!(
+        std::fs::read_to_string(collision).unwrap(),
+        "This file makes 'external' a real directory in CARGO_MANIFEST_DIR."
+    );
+}