diff --git a/cleanup.go b/cleanup.go
index 35340f5..a1a3a71 100644
--- a/cleanup.go
+++ b/cleanup.go
@@ -26,8 +26,9 @@ func cleanupOrphanedRepos(config *mirror.RepoPoolConfig, repoPool *mirror.RepoPo
 	}
 
 	repoDirs := repoPool.RepositoriesDirPath()
+	defaultRepoDirRoot := mirror.DefaultRepoDir(config.Defaults.Root)
 
-	entries, err := os.ReadDir(config.Defaults.Root)
+	entries, err := os.ReadDir(defaultRepoDirRoot)
 	if err != nil {
 		logger.Error("unable to read root dir for clean up", "err", err)
 		return
@@ -38,7 +39,7 @@ func cleanupOrphanedRepos(config *mirror.RepoPoolConfig, repoPool *mirror.RepoPo
 			continue
 		}
 
-		fullPath := filepath.Join(config.Defaults.Root, entry.Name())
+		fullPath := filepath.Join(defaultRepoDirRoot, entry.Name())
 
 		if slices.Contains(repoDirs, fullPath) {
 			continue
diff --git a/pkg/mirror/config.go b/pkg/mirror/config.go
index e92f23e..3fd27ed 100644
--- a/pkg/mirror/config.go
+++ b/pkg/mirror/config.go
@@ -125,6 +125,11 @@ func (rpc *RepoPoolConfig) ValidateDefaults() error {
 	return nil
 }
 
+// DefaultRepoDir returns path of dir where all repositories mirrors are cloned
+func DefaultRepoDir(root string) string {
+	return filepath.Join(root, "repo-mirrors")
+}
+
 // ApplyDefaults will add  given default config to repository config if where needed
 func (rpc *RepoPoolConfig) ApplyDefaults() {
 	for i := range rpc.Repositories {
diff --git a/pkg/mirror/repository.go b/pkg/mirror/repository.go
index dba97bb..faf98f9 100644
--- a/pkg/mirror/repository.go
+++ b/pkg/mirror/repository.go
@@ -105,7 +105,7 @@ func NewRepository(repoConf RepositoryConfig, envs []string, log *slog.Logger) (
 	if !strings.HasSuffix(repoDir, ".git") {
 		repoDir += ".git"
 	}
-	repoDir = filepath.Join(repoConf.Root, repoDir)
+	repoDir = filepath.Join(DefaultRepoDir(repoConf.Root), repoDir)
 
 	repo := &Repository{
 		gitURL:        gURL,
diff --git a/pkg/mirror/repository_test.go b/pkg/mirror/repository_test.go
index 309aa78..6921259 100644
--- a/pkg/mirror/repository_test.go
+++ b/pkg/mirror/repository_test.go
@@ -37,7 +37,7 @@ func TestNewRepo(t *testing.T) {
 				gitURL:        &giturl.URL{Scheme: "scp", User: "user", Host: "host.xz", Path: "path/to", Repo: "repo.git"},
 				remote:        "user@host.xz:path/to/repo.git",
 				root:          "/tmp",
-				dir:           "/tmp/repo.git",
+				dir:           "/tmp/repo-mirrors/repo.git",
 				gitGC:         "always",
 				interval:      10 * time.Second,
 				auth:          &Auth{SSHKeyPath: "/path/to/key", SSHKnownHostsPath: "path/to/host"},