diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
index dbf8eb780..ed32c638e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java
@@ -997,6 +997,9 @@ private void deleteOrphans() {
 	private void deleteTempPacksIdx() {
 		Path packDir = repo.getObjectDatabase().getPackDirectory().toPath();
 		Instant threshold = Instant.now().minus(1, ChronoUnit.DAYS);
+		if (!Files.exists(packDir)) {
+			return;
+		}
 		try (DirectoryStream<Path> stream =
 				Files.newDirectoryStream(packDir, "gc_*_tmp")) { //$NON-NLS-1$
 			stream.forEach(t -> {
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
index 9b2865d85..6a18df86e 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/RefDirectory.java
@@ -1287,7 +1287,7 @@ private static void delete(File file, int depth, LockFile rLck)
 		File dir = file.getParentFile();
 		for (int i = 0; i < depth; ++i) {
 			try {
-				Files.delete(dir.toPath());
+				Files.deleteIfExists(dir.toPath());
 			} catch (DirectoryNotEmptyException e) {
 				// Don't log; normal case when there are other refs with the
 				// same prefix