diff --git a/internal/project/auto/git.go b/internal/project/auto/git.go
index 851065cc..59cf96b7 100644
--- a/internal/project/auto/git.go
+++ b/internal/project/auto/git.go
@@ -16,7 +16,9 @@ import (
 
 // DetectGit detects if current directory is git repository.
 func (builder *builder) DetectGit() (bool, error) {
-	repo, err := git.PlainOpen(".")
+	repo, err := git.PlainOpenWithOptions(".", &git.PlainOpenOptions{
+		EnableDotGitCommonDir: true,
+	})
 	if err != nil {
 		// not a git repo, ignore
 		return false, nil //nolint:nilerr
diff --git a/internal/project/auto/git_test.go b/internal/project/auto/git_test.go
new file mode 100644
index 00000000..fdfcfb1a
--- /dev/null
+++ b/internal/project/auto/git_test.go
@@ -0,0 +1,66 @@
+// This Source Code Form is subject to the terms of the Mozilla Public
+// License, v. 2.0. If a copy of the MPL was not distributed with this
+// file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+package auto_test
+
+import (
+	"context"
+	"os/exec"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/siderolabs/kres/internal/project/auto"
+	"github.com/siderolabs/kres/internal/project/meta"
+)
+
+func TestDetectGitWorktree(t *testing.T) {
+	if _, err := exec.LookPath("git"); err != nil {
+		t.Skip("git not found")
+	}
+
+	root := filepath.Join(t.TempDir(), "repo")
+	worktree := filepath.Join(t.TempDir(), "worktree")
+
+	runGit(t, "", "init", root)
+	runGit(t, root, "config", "user.email", "test@example.com")
+	runGit(t, root, "config", "user.name", "Test")
+	runGit(t, root, "config", "commit.gpgsign", "false")
+	runGit(t, root, "commit", "--allow-empty", "-m", "init")
+	runGit(t, root, "branch", "-M", "main")
+	runGit(t, root, "remote", "add", "origin", "git@github.com:siderolabs/example.git")
+	runGit(t, root, "config", "branch.main.remote", "origin")
+	runGit(t, root, "config", "branch.main.merge", "refs/heads/main")
+	runGit(t, root, "worktree", "add", "-b", "feature", worktree)
+
+	t.Chdir(worktree)
+
+	options := &meta.Options{
+		CompileGithubWorkflowsOnly: true,
+	}
+
+	_, err := auto.Build(options)
+	require.NoError(t, err)
+
+	assert.Equal(t, "main", options.MainBranch)
+	assert.Equal(t, "feature", options.CurrentBranch)
+	assert.Equal(t, "siderolabs", options.GitHubOrganization)
+	assert.Equal(t, "example", options.GitHubRepository)
+}
+
+func runGit(t *testing.T, dir string, args ...string) {
+	t.Helper()
+
+	ctx, cancel := context.WithTimeout(context.Background(), time.Minute)
+	defer cancel()
+
+	cmd := exec.CommandContext(ctx, "git", args...)
+	cmd.Dir = dir
+
+	output, err := cmd.CombinedOutput()
+	require.NoError(t, err, string(output))
+}