diff --git a/CHANGELOG.md b/CHANGELOG.md
index d7403b4f1a..5a71e5f972 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -75,6 +75,8 @@ END_UNRELEASED_TEMPLATE
   underlying runtime.
 * (performance) 90% reduction in py_binary/py_test analysis phase cost.
   ([#3381](https://github.com/bazel-contrib/rules_python/pull/3381)).
+* (gazelle) Fix `gazelle_python_manifest.test` so that it accesses manifest files via `runfile` path handling rather than directly ([#3397](https://github.com/bazel-contrib/rules_python/issues/3397)).
+
 
 {#v0-0-0-added}
 ### Added
diff --git a/gazelle/manifest/defs.bzl b/gazelle/manifest/defs.bzl
index 45fdb32e7d..b615c4efc1 100644
--- a/gazelle/manifest/defs.bzl
+++ b/gazelle/manifest/defs.bzl
@@ -117,9 +117,9 @@ def gazelle_python_manifest(
     if requirements:
         attrs = {
             "env": {
-                "_TEST_MANIFEST": "$(rootpath {})".format(manifest),
+                "_TEST_MANIFEST": "$(rlocationpath {})".format(manifest),
                 "_TEST_MANIFEST_GENERATOR_HASH": "$(rlocationpath {})".format(manifest_generator_hash),
-                "_TEST_REQUIREMENTS": "$(rootpath {})".format(requirements),
+                "_TEST_REQUIREMENTS": "$(rlocationpath {})".format(requirements),
             },
             "size": "small",
         }
diff --git a/gazelle/manifest/test/test.go b/gazelle/manifest/test/test.go
index 5804a7102e..77b354b495 100644
--- a/gazelle/manifest/test/test.go
+++ b/gazelle/manifest/test/test.go
@@ -26,23 +26,32 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/bazelbuild/rules_go/go/runfiles"
 	"github.com/bazel-contrib/rules_python/gazelle/manifest"
+	"github.com/bazelbuild/rules_go/go/runfiles"
 )
 
-func TestGazelleManifestIsUpdated(t *testing.T) {
-	requirementsPath := os.Getenv("_TEST_REQUIREMENTS")
-	if requirementsPath == "" {
-		t.Fatal("_TEST_REQUIREMENTS must be set")
+// getResolvedRunfile resolves an environment variable to a runfiles path.
+// It handles getting the env var, checking it's set, and resolving it through
+// the runfiles mechanism, providing detailed error messages if anything fails.
+func getResolvedRunfile(t *testing.T, envVar string) string {
+	t.Helper()
+	path := os.Getenv(envVar)
+	if path == "" {
+		t.Fatalf("%s must be set", envVar)
 	}
-
-	manifestPath := os.Getenv("_TEST_MANIFEST")
-	if manifestPath == "" {
-		t.Fatal("_TEST_MANIFEST must be set")
+	resolvedPath, err := runfiles.Rlocation(path)
+	if err != nil {
+		t.Fatalf("failed to resolve runfiles path for %s (%q): %v", envVar, path, err)
 	}
+	return resolvedPath
+}
+
+func TestGazelleManifestIsUpdated(t *testing.T) {
+	requirementsPathResolved := getResolvedRunfile(t, "_TEST_REQUIREMENTS")
+	manifestPathResolved := getResolvedRunfile(t, "_TEST_MANIFEST")
 
 	manifestFile := new(manifest.File)
-	if err := manifestFile.Decode(manifestPath); err != nil {
+	if err := manifestFile.Decode(manifestPathResolved); err != nil {
 		t.Fatalf("decoding manifest file: %v", err)
 	}
 
@@ -50,11 +59,7 @@ func TestGazelleManifestIsUpdated(t *testing.T) {
 		t.Fatal("failed to find the Gazelle manifest file integrity")
 	}
 
-	manifestGeneratorHashPath, err := runfiles.Rlocation(
-		os.Getenv("_TEST_MANIFEST_GENERATOR_HASH"))
-	if err != nil {
-		t.Fatalf("failed to resolve runfiles path of manifest: %v", err)
-	}
+	manifestGeneratorHashPath := getResolvedRunfile(t, "_TEST_MANIFEST_GENERATOR_HASH")
 
 	manifestGeneratorHash, err := os.Open(manifestGeneratorHashPath)
 	if err != nil {
@@ -62,9 +67,9 @@ func TestGazelleManifestIsUpdated(t *testing.T) {
 	}
 	defer manifestGeneratorHash.Close()
 
-	requirements, err := os.Open(requirementsPath)
+	requirements, err := os.Open(requirementsPathResolved)
 	if err != nil {
-		t.Fatalf("opening %q: %v", requirementsPath, err)
+		t.Fatalf("opening %q: %v", requirementsPathResolved, err)
 	}
 	defer requirements.Close()
 
@@ -73,9 +78,9 @@ func TestGazelleManifestIsUpdated(t *testing.T) {
 		t.Fatalf("verifying integrity: %v", err)
 	}
 	if !valid {
-		manifestRealpath, err := filepath.EvalSymlinks(manifestPath)
+		manifestRealpath, err := filepath.EvalSymlinks(manifestPathResolved)
 		if err != nil {
-			t.Fatalf("evaluating symlink %q: %v", manifestPath, err)
+			t.Fatalf("evaluating symlink %q: %v", manifestPathResolved, err)
 		}
 		t.Errorf(
 			"%q is out-of-date. Follow the update instructions in that file to resolve this",