diff --git a/.github/workflows/java.yaml b/.github/workflows/java.yaml
index 628b950cf7e..26cac0765ed 100644
--- a/.github/workflows/java.yaml
+++ b/.github/workflows/java.yaml
@@ -116,7 +116,7 @@ jobs:
         working-directory: google-cloud-java
         run: librarian generate secretmanager
       - name: Run librarian generate all (integration test)
-        if: matrix.task == 'integration' && github.event_name == 'push' && github.ref == 'refs/heads/main'
+        if: matrix.task == 'integration'
         working-directory: google-cloud-java
         run: librarian generate --all
   create-issue-on-failure:
diff --git a/internal/librarian/java/format.go b/internal/librarian/java/format.go
index 70894f1bb4b..45194375695 100644
--- a/internal/librarian/java/format.go
+++ b/internal/librarian/java/format.go
@@ -61,7 +61,14 @@ func collectJavaFiles(root string) ([]string, error) {
 		if err != nil {
 			return err
 		}
-		if d.IsDir() || filepath.Ext(path) != ".java" {
+		if d.IsDir() {
+			name := d.Name()
+			if name == "target" || (strings.HasPrefix(name, ".") && name != ".") || strings.HasPrefix(name, "proto-") || strings.HasPrefix(name, "grpc-") {
+				return filepath.SkipDir
+			}
+			return nil
+		}
+		if filepath.Ext(path) != ".java" {
 			return nil
 		}
 		// Exclude generated samples and Spanner-specific sample source directory.