diff --git a/pkg/external/customtemplates/github.go b/pkg/external/customtemplates/github.go
index ee30f34565..dc75c5e94e 100644
--- a/pkg/external/customtemplates/github.go
+++ b/pkg/external/customtemplates/github.go
@@ -13,6 +13,7 @@ import (
 	"github.com/projectdiscovery/nuclei/v3/pkg/catalog/config"
 	"github.com/projectdiscovery/nuclei/v3/pkg/types"
 	fileutil "github.com/projectdiscovery/utils/file"
+	folderutil "github.com/projectdiscovery/utils/folder"
 	"golang.org/x/oauth2"
 	"gopkg.in/src-d/go-git.v4/plumbing/transport/http"
 )
@@ -85,10 +86,22 @@ func NewGitHubProviders(options *types.Options) ([]*customTemplateGitHubRepo, er
 			githubToken: options.GitHubToken,
 		}
 		providers = append(providers, customTemplateRepo)
+
+		customTemplateRepo.restructureRepoDir()
 	}
 	return providers, nil
 }
 
+func (customTemplateRepo *customTemplateGitHubRepo) restructureRepoDir() {
+	customGitHubTemplatesDirectory := config.DefaultConfig.CustomGitHubTemplatesDirectory
+	oldRepoClonePath := filepath.Join(customGitHubTemplatesDirectory, customTemplateRepo.reponame+"-"+customTemplateRepo.owner)
+	newRepoClonePath := customTemplateRepo.getLocalRepoClonePath(customGitHubTemplatesDirectory)
+
+	if fileutil.FolderExists(oldRepoClonePath) && !fileutil.FolderExists(newRepoClonePath) {
+		_ = folderutil.SyncDirectory(oldRepoClonePath, newRepoClonePath)
+	}
+}
+
 // getOwnerAndRepo returns the owner, repo, err from the given string
 // e.g., it takes input projectdiscovery/nuclei-templates and
 // returns owner => projectdiscovery, repo => nuclei-templates
@@ -154,9 +167,9 @@ func (ctr *customTemplateGitHubRepo) pullChanges(repoPath, githubToken string) e
 	return nil
 }
 
-// All Custom github repos are cloned in the format of 'reponame-owner' for uniqueness
+// All Custom github repos are cloned in the format of 'owner/reponame' for uniqueness
 func (ctr *customTemplateGitHubRepo) getLocalRepoClonePath(downloadPath string) string {
-	return filepath.Join(downloadPath, ctr.reponame+"-"+ctr.owner)
+	return filepath.Join(downloadPath, ctr.owner, ctr.reponame)
 }
 
 // returns the auth object with username and github token as password
diff --git a/pkg/external/customtemplates/github_test.go b/pkg/external/customtemplates/github_test.go
index ab070c7a34..2f55800be6 100644
--- a/pkg/external/customtemplates/github_test.go
+++ b/pkg/external/customtemplates/github_test.go
@@ -30,6 +30,6 @@ func TestDownloadCustomTemplatesFromGitHub(t *testing.T) {
 
 	ctm.Download(context.Background())
 
-	require.DirExists(t, filepath.Join(templatesDirectory, "github", "nuclei-templates-projectdiscovery"), "cloned directory does not exists")
-	require.DirExists(t, filepath.Join(templatesDirectory, "github", "nuclei-templates-ehsandeep"), "cloned directory does not exists")
+	require.DirExists(t, filepath.Join(templatesDirectory, "github", "projectdiscovery", "nuclei-templates"), "cloned directory does not exists")
+	require.DirExists(t, filepath.Join(templatesDirectory, "github", "ehsandeep", "nuclei-templates"), "cloned directory does not exists")
 }