diff --git a/src/main/java/org/cryptomator/cryptofs/CryptoFileSystemImpl.java b/src/main/java/org/cryptomator/cryptofs/CryptoFileSystemImpl.java
index 8bd83d2d..d3d7af7c 100644
--- a/src/main/java/org/cryptomator/cryptofs/CryptoFileSystemImpl.java
+++ b/src/main/java/org/cryptomator/cryptofs/CryptoFileSystemImpl.java
@@ -18,6 +18,7 @@
 import org.cryptomator.cryptofs.common.DeletingFileVisitor;
 import org.cryptomator.cryptofs.common.FinallyUtil;
 import org.cryptomator.cryptofs.dir.CiphertextDirectoryDeleter;
+import org.cryptomator.cryptofs.dir.DirectoryStreamFilters;
 import org.cryptomator.cryptofs.dir.DirectoryStreamFactory;
 import org.cryptomator.cryptofs.fh.OpenCryptoFiles;
 import org.cryptomator.cryptolib.api.Cryptor;
@@ -621,20 +622,21 @@ private void moveDirectory(CryptoPath cleartextSource, CryptoPath cleartextTarge
 				throw new AtomicMoveNotSupportedException(cleartextSource.toString(), cleartextTarget.toString(), "Replacing directories during move requires non-atomic status checks.");
 			}
 			// check if dir is empty:
-			Path oldCiphertextDir = cryptoPathMapper.getCiphertextDir(cleartextTarget).path;
-			boolean oldCiphertextDirExists = true;
-			try (DirectoryStream<Path> ds = Files.newDirectoryStream(oldCiphertextDir)) {
+			Path targetCiphertextDirContentDir = cryptoPathMapper.getCiphertextDir(cleartextTarget).path;
+			boolean targetCiphertextDirExists = true;
+			try (DirectoryStream<Path> ds = Files.newDirectoryStream(targetCiphertextDirContentDir, DirectoryStreamFilters.EXCLUDE_DIR_ID_BACKUP)) {
 				if (ds.iterator().hasNext()) {
 					throw new DirectoryNotEmptyException(cleartextTarget.toString());
 				}
 			} catch (NoSuchFileException e) {
-				oldCiphertextDirExists = false;
-			}
-			// cleanup dir to be replaced:
-			if (oldCiphertextDirExists) {
-				Files.walkFileTree(oldCiphertextDir, DeletingFileVisitor.INSTANCE);
+				targetCiphertextDirExists = false;
 			}
+			//delete dir link
 			Files.walkFileTree(ciphertextTarget.getRawPath(), DeletingFileVisitor.INSTANCE);
+			// cleanup content dir
+			if (targetCiphertextDirExists) {
+				Files.walkFileTree(targetCiphertextDirContentDir, DeletingFileVisitor.INSTANCE);
+			}
 		}
 
 		// no exceptions until this point, so MOVE:
diff --git a/src/main/java/org/cryptomator/cryptofs/dir/DirectoryStreamFilters.java b/src/main/java/org/cryptomator/cryptofs/dir/DirectoryStreamFilters.java
new file mode 100644
index 00000000..13f87c11
--- /dev/null
+++ b/src/main/java/org/cryptomator/cryptofs/dir/DirectoryStreamFilters.java
@@ -0,0 +1,12 @@
+package org.cryptomator.cryptofs.dir;
+
+import org.cryptomator.cryptofs.common.Constants;
+
+import java.nio.file.DirectoryStream;
+import java.nio.file.Path;
+
+public interface DirectoryStreamFilters {
+
+	static DirectoryStream.Filter<Path> EXCLUDE_DIR_ID_BACKUP = p -> !p.equals(p.resolveSibling(Constants.DIR_BACKUP_FILE_NAME));
+
+}
diff --git a/src/test/java/org/cryptomator/cryptofs/CryptoFileSystemProviderInMemoryIntegrationTest.java b/src/test/java/org/cryptomator/cryptofs/CryptoFileSystemProviderInMemoryIntegrationTest.java
index c2822284..6b494ebb 100644
--- a/src/test/java/org/cryptomator/cryptofs/CryptoFileSystemProviderInMemoryIntegrationTest.java
+++ b/src/test/java/org/cryptomator/cryptofs/CryptoFileSystemProviderInMemoryIntegrationTest.java
@@ -58,6 +58,21 @@ public static void afterAll() throws IOException {
 		tmpFs.close();
 	}
 
+	@Test
+	@DisplayName("Replace an existing, shortened, empty directory")
+	public void testReplaceExistingShortenedDirEmpty() throws IOException {
+		try (var fs = setupCryptoFs(50, 100, false)) {
+			var dirName50Chars = "/target_89_123456789_123456789_123456789_123456789_"; //since filename encryption increases filename length, 50 cleartext chars are sufficient
+			var source = fs.getPath("/sourceDir");
+			var target = fs.getPath(dirName50Chars);
+			Files.createDirectory(source);
+			Files.createDirectory(target);
+			assertDoesNotThrow(() -> Files.move(source, target, REPLACE_EXISTING));
+			assertTrue(Files.notExists(source));
+			assertTrue(Files.exists(target));
+		}
+	}
+
 	@Test
 	@DisplayName("Replace an existing, shortened file")
 	public void testReplaceExistingShortenedFile() throws IOException {