diff --git a/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/DefaultGitRepositoryService.java b/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/DefaultGitRepositoryService.java
index 0788143030..2aa31e194d 100644
--- a/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/DefaultGitRepositoryService.java
+++ b/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/DefaultGitRepositoryService.java
@@ -203,7 +203,7 @@ public class DefaultGitRepositoryService implements GitRepositoryService {
         GitRepository gitRepository = Optional.ofNullable(repositories.get(tenantId))
                 .orElseThrow(() -> new IllegalStateException("Repository is not initialized"));
 
-        if (!Files.exists(Path.of(gitRepository.getDirectory()))) {
+        if (!GitRepository.exists(gitRepository.getDirectory())) {
             try {
                 return openOrCloneRepository(tenantId, gitRepository.getSettings(), false);
             } catch (Exception e) {
@@ -285,12 +285,13 @@ public class DefaultGitRepositoryService implements GitRepositoryService {
         Path repositoryDirectory = Path.of(repositoriesFolder, settings.isLocalOnly() ? "local_" + settings.getRepositoryUri() : tenantId.getId().toString());
 
         GitRepository repository;
-        if (Files.exists(repositoryDirectory)) {
+        if (GitRepository.exists(repositoryDirectory.toString())) {
             repository = GitRepository.open(repositoryDirectory.toFile(), settings);
             if (fetch) {
                 repository.fetch();
             }
         } else {
+            FileUtils.deleteDirectory(repositoryDirectory.toFile());
             Files.createDirectories(repositoryDirectory);
             if (settings.isLocalOnly()) {
                 repository = GitRepository.create(settings, repositoryDirectory.toFile());
diff --git a/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/GitRepository.java b/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/GitRepository.java
index aaa4c22289..2ff6a97c21 100644
--- a/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/GitRepository.java
+++ b/common/version-control/src/main/java/org/thingsboard/server/service/sync/vc/GitRepository.java
@@ -21,6 +21,7 @@ import com.google.common.collect.Streams;
 import lombok.Data;
 import lombok.Getter;
 import lombok.RequiredArgsConstructor;
+import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
@@ -75,6 +76,7 @@ import java.io.IOException;
 import java.net.InetSocketAddress;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
+import java.nio.file.Path;
 import java.security.KeyPair;
 import java.security.PublicKey;
 import java.util.ArrayList;
@@ -409,6 +411,12 @@ public class GitRepository {
         return result;
     }
 
+    @SneakyThrows
+    public static boolean exists(String directory) {
+        File gitDirectory = Path.of(directory, ".git").toFile();
+        return FileUtils.isDirectory(gitDirectory) && !FileUtils.isEmptyDirectory(gitDirectory);
+    }
+
     private <C extends GitCommand<T>, T> T execute(C command) throws GitAPIException {
         if (command instanceof TransportCommand transportCommand && authHandler != null) {
             authHandler.configureCommand(transportCommand);