diff --git a/modules/git/repo.go b/modules/git/repo.go
index 61930ab31db96..5681d39c3b717 100644
--- a/modules/git/repo.go
+++ b/modules/git/repo.go
@@ -80,7 +80,7 @@ func InitRepository(ctx context.Context, repoPath string, bare bool) error {
 // IsEmpty Check if repository is empty.
 func (repo *Repository) IsEmpty() (bool, error) {
 	var errbuf, output strings.Builder
-	if err := NewCommand(repo.Ctx).AddOptionFormat("--git-dir=%s", repo.Path).AddArguments("show-ref", "--head", "^HEAD$").
+	if err := NewCommand(repo.Ctx).AddOptionFormat("--git-dir=%s", repo.Path).AddArguments("rev-list", "-n", "1", "--all").
 		Run(&RunOpts{
 			Dir:    repo.Path,
 			Stdout: &output,
diff --git a/routers/web/repo/editor.go b/routers/web/repo/editor.go
index b5129b730b67a..b053e3c63f4a7 100644
--- a/routers/web/repo/editor.go
+++ b/routers/web/repo/editor.go
@@ -370,7 +370,9 @@ func editFilePost(ctx *context.Context, form forms.EditRepoFileForm, isNewFile b
 	}
 
 	if ctx.Repo.Repository.IsEmpty {
-		_ = repo_model.UpdateRepositoryCols(ctx, &repo_model.Repository{ID: ctx.Repo.Repository.ID, IsEmpty: false}, "is_empty")
+		if isEmpty, err := ctx.Repo.GitRepo.IsEmpty(); err == nil && !isEmpty {
+			_ = repo_model.UpdateRepositoryCols(ctx, &repo_model.Repository{ID: ctx.Repo.Repository.ID, IsEmpty: false}, "is_empty")
+		}
 	}
 
 	redirectForCommitChoice(ctx, form.CommitChoice, branchName, form.TreePath)
@@ -763,7 +765,9 @@ func UploadFilePost(ctx *context.Context) {
 	}
 
 	if ctx.Repo.Repository.IsEmpty {
-		_ = repo_model.UpdateRepositoryCols(ctx, &repo_model.Repository{ID: ctx.Repo.Repository.ID, IsEmpty: false}, "is_empty")
+		if isEmpty, err := ctx.Repo.GitRepo.IsEmpty(); err == nil && !isEmpty {
+			_ = repo_model.UpdateRepositoryCols(ctx, &repo_model.Repository{ID: ctx.Repo.Repository.ID, IsEmpty: false}, "is_empty")
+		}
 	}
 
 	redirectForCommitChoice(ctx, form.CommitChoice, branchName, form.TreePath)
diff --git a/services/repository/files/update.go b/services/repository/files/update.go
index cd7713341dce8..f01092d360d6c 100644
--- a/services/repository/files/update.go
+++ b/services/repository/files/update.go
@@ -263,7 +263,9 @@ func ChangeRepoFiles(ctx context.Context, repo *repo_model.Repository, doer *use
 	}
 
 	if repo.IsEmpty {
-		_ = repo_model.UpdateRepositoryCols(ctx, &repo_model.Repository{ID: repo.ID, IsEmpty: false, DefaultBranch: opts.NewBranch}, "is_empty", "default_branch")
+		if isEmpty, err := gitRepo.IsEmpty(); err == nil && !isEmpty {
+			_ = repo_model.UpdateRepositoryCols(ctx, &repo_model.Repository{ID: repo.ID, IsEmpty: false, DefaultBranch: opts.NewBranch}, "is_empty", "default_branch")
+		}
 	}
 
 	return filesResponse, nil