diff --git a/retrieval/discovery/file.go b/retrieval/discovery/file.go
index c0251a510..25201dd77 100644
--- a/retrieval/discovery/file.go
+++ b/retrieval/discovery/file.go
@@ -247,9 +247,10 @@ func readFile(filename string) ([]*config.TargetGroup, error) {
 
 	for i, tg := range targetGroups {
 		tg.Source = fileSource(filename, i)
-		tg.Labels = clientmodel.LabelSet{
-			FileSDFilepathLabel: clientmodel.LabelValue(filename),
+		if tg.Labels == nil {
+			tg.Labels = clientmodel.LabelSet{}
 		}
+		tg.Labels[FileSDFilepathLabel] = clientmodel.LabelValue(filename)
 	}
 	return targetGroups, nil
 }
diff --git a/retrieval/discovery/file_test.go b/retrieval/discovery/file_test.go
index 8ae0ef8ab..89de0cb0a 100644
--- a/retrieval/discovery/file_test.go
+++ b/retrieval/discovery/file_test.go
@@ -11,10 +11,10 @@ import (
 )
 
 func TestFileSD(t *testing.T) {
+	defer os.Remove("fixtures/_test.yml")
+	defer os.Remove("fixtures/_test.json")
 	testFileSD(t, ".yml")
 	testFileSD(t, ".json")
-	os.Remove("fixtures/_test.yml")
-	os.Remove("fixtures/_test.json")
 }
 
 func testFileSD(t *testing.T, ext string) {
@@ -60,6 +60,9 @@ func testFileSD(t *testing.T, ext string) {
 	case <-time.After(15 * time.Second):
 		t.Fatalf("Expected new target group but got none")
 	case tg := <-ch:
+		if _, ok := tg.Labels["foo"]; !ok {
+			t.Fatalf("Label not parsed")
+		}
 		if tg.String() != fmt.Sprintf("file:fixtures/_test%s:0", ext) {
 			t.Fatalf("Unexpected target group", tg)
 		}
diff --git a/retrieval/discovery/fixtures/target_groups.yml b/retrieval/discovery/fixtures/target_groups.yml
index a4823b2b9..5a4e6e5db 100644
--- a/retrieval/discovery/fixtures/target_groups.yml
+++ b/retrieval/discovery/fixtures/target_groups.yml
@@ -1,5 +1,5 @@
 - targets: ['localhost:9090', 'example.org:443']
   labels:
-    test: success
+    foo: bar
 
 - targets: ['my.domain']