diff --git a/CHANGELOG.md b/CHANGELOG.md
index 035181e..5e129ea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,8 @@
 
 ## Unreleased
 
+- Create a missing local database during `init` when the path is inside a Git worktree. Leave an existing database unchanged, and leave a gzip portable source without a raw database file unchanged. Thanks @SebTardif.
+
 ## 0.15.1 - 2026-10-11
 
 **Highlights:** Faster embedding on large archives, reliable local database setup, and Go security fixes.
diff --git a/internal/cli/init.go b/internal/cli/init.go
index 8c37142..ea079e4 100644
--- a/internal/cli/init.go
+++ b/internal/cli/init.go
@@ -2,9 +2,11 @@ package cli
 
 import (
 	"context"
+	"errors"
 	"flag"
 	"fmt"
 	"io"
+	"os"
 	"path/filepath"
 	"strings"
 
@@ -118,22 +120,13 @@ func (a *App) runInit(ctx context.Context, args []string) error {
 	if err := config.Save(a.configPath, cfg); err != nil {
 		return err
 	}
-	if !(cfg.Remote.Enabled() && cfg.Remote.Mode == crawlremote.ModeCloud) {
-		if err := config.EnsureRuntimeDirs(cfg); err != nil {
+	if remoteEndpointValue == "" && portableStoreURL == "" {
+		if err := initializeMissingLocalDatabase(ctx, cfg); err != nil {
 			return err
 		}
-	}
-	if remoteEndpointValue == "" && portableStoreURL == "" {
-		if _, portable, err := portableStoreRoot(ctx, cfg.DBPath); err != nil {
+	} else if !(cfg.Remote.Enabled() && cfg.Remote.Mode == crawlremote.ModeCloud) {
+		if err := config.EnsureRuntimeDirs(cfg); err != nil {
 			return err
-		} else if !portable {
-			st, err := store.Open(ctx, cfg.DBPath)
-			if err != nil {
-				return fmt.Errorf("initialize local database: %w", err)
-			}
-			if err := st.Close(); err != nil {
-				return fmt.Errorf("close initialized local database: %w", err)
-			}
 		}
 	}
 	result := initResult{
@@ -155,6 +148,53 @@ func (a *App) runInit(ctx context.Context, args []string) error {
 	return a.writeInitOutput(result)
 }
 
+// initializeMissingLocalDatabase creates the local SQLite file when it is
+// absent. An existing file inside a Git worktree is left untouched, as is a
+// missing raw file whose manifest selects a gzip archive. Opening either
+// would migrate or dirty an unmarked portable source.
+func initializeMissingLocalDatabase(ctx context.Context, cfg config.Config) error {
+	preserve, err := preservePortableDatabase(ctx, cfg.DBPath)
+	if err != nil {
+		return err
+	}
+	if preserve {
+		return nil
+	}
+	if err := config.EnsureRuntimeDirs(cfg); err != nil {
+		return err
+	}
+	st, err := store.Open(ctx, cfg.DBPath)
+	if err != nil {
+		return fmt.Errorf("initialize local database: %w", err)
+	}
+	if err := st.Close(); err != nil {
+		return fmt.Errorf("close initialized local database: %w", err)
+	}
+	return nil
+}
+
+func preservePortableDatabase(ctx context.Context, dbPath string) (bool, error) {
+	_, portable, err := portableStoreRoot(ctx, dbPath)
+	if err != nil {
+		return false, err
+	}
+	if !portable {
+		return false, nil
+	}
+	_, err = os.Stat(dbPath)
+	if err == nil {
+		return true, nil
+	}
+	if !errors.Is(err, os.ErrNotExist) {
+		return false, fmt.Errorf("inspect local database: %w", err)
+	}
+	_, _, compressed, err := portableSourceArtifact(dbPath)
+	if err != nil {
+		return false, err
+	}
+	return compressed, nil
+}
+
 func (a *App) absoluteInitPath(path string) (string, error) {
 	originalPath := strings.TrimSpace(path)
 	path = crawlconfig.ExpandHome(path)
diff --git a/internal/cli/init_worktree_test.go b/internal/cli/init_worktree_test.go
new file mode 100644
index 0000000..71b01f2
--- /dev/null
+++ b/internal/cli/init_worktree_test.go
@@ -0,0 +1,131 @@
+package cli
+
+import (
+	"bytes"
+	"context"
+	"errors"
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/openclaw/gitcrawl/internal/store"
+)
+
+func TestInitCreatesMissingDatabaseInsideGitWorktree(t *testing.T) {
+	ctx := context.Background()
+
+	t.Run("db flag", func(t *testing.T) {
+		repo := initOrdinaryGitRepo(t, ctx)
+		dbPath := filepath.Join(repo, "gitcrawl.db")
+		assertOrdinaryGitWorktree(t, ctx, repo, dbPath)
+		configPath := filepath.Join(repo, "config.toml")
+		if err := New().Run(ctx, []string{"--config", configPath, "init", "--db", dbPath}); err != nil {
+			t.Fatalf("init: %v", err)
+		}
+		assertInitializedLocalDatabase(t, ctx, dbPath)
+		if err := New().Run(ctx, []string{"--config", configPath, "doctor"}); err != nil {
+			t.Fatalf("doctor: %v", err)
+		}
+	})
+
+	t.Run("runtime dir", func(t *testing.T) {
+		repo := initOrdinaryGitRepo(t, ctx)
+		runtimeDir := filepath.Join(repo, "runtime")
+		dbPath := filepath.Join(runtimeDir, "gitcrawl.db")
+		assertOrdinaryGitWorktree(t, ctx, repo, dbPath)
+		configPath := filepath.Join(repo, "config.toml")
+		if err := New().Run(ctx, []string{"--config", configPath, "init", "--runtime-dir", runtimeDir}); err != nil {
+			t.Fatalf("init: %v", err)
+		}
+		assertInitializedLocalDatabase(t, ctx, dbPath)
+		if err := New().Run(ctx, []string{"--config", configPath, "doctor"}); err != nil {
+			t.Fatalf("doctor: %v", err)
+		}
+	})
+}
+
+func TestInitLeavesExistingWorktreeDatabaseUntouched(t *testing.T) {
+	ctx := context.Background()
+	repo := initOrdinaryGitRepo(t, ctx)
+	dbPath := filepath.Join(repo, "gitcrawl.db")
+	assertOrdinaryGitWorktree(t, ctx, repo, dbPath)
+	const sentinel = "not a gitcrawl database\n"
+	if err := os.WriteFile(dbPath, []byte(sentinel), 0o644); err != nil {
+		t.Fatalf("write sentinel: %v", err)
+	}
+	configPath := filepath.Join(repo, "config.toml")
+	if err := New().Run(ctx, []string{"--config", configPath, "init", "--db", dbPath}); err != nil {
+		t.Fatalf("init: %v", err)
+	}
+	got, err := os.ReadFile(dbPath)
+	if err != nil {
+		t.Fatalf("read database: %v", err)
+	}
+	if string(got) != sentinel {
+		t.Fatalf("existing worktree database changed to %q", got)
+	}
+}
+
+func TestInitDBPreservesCompressedPortableCheckout(t *testing.T) {
+	fixture := newPortableRefreshFixture(t, true)
+	logical := filepath.Join(fixture.checkout, fixture.relative)
+	if _, err := os.Stat(logical); !errors.Is(err, os.ErrNotExist) {
+		t.Fatalf("fixture raw database: %v", err)
+	}
+	before := portableTestGit(t, fixture.checkout, "status", "--porcelain=v1", "-z", "--untracked-files=all", "--ignored=matching")
+	if before != "" {
+		t.Fatalf("fixture not clean: %q", before)
+	}
+	configPath := filepath.Join(filepath.Dir(fixture.checkout), "local.toml")
+	app := New()
+	var stdout, stderr bytes.Buffer
+	app.Stdout, app.Stderr = &stdout, &stderr
+	if err := app.Run(context.Background(), []string{"--config", configPath, "init", "--db", logical}); err != nil {
+		t.Fatalf("init: %v\n%s", err, stderr.String())
+	}
+	if _, err := os.Stat(logical); !errors.Is(err, os.ErrNotExist) {
+		t.Fatalf("init created raw database: %v", err)
+	}
+	after := portableTestGit(t, fixture.checkout, "status", "--porcelain=v1", "-z", "--untracked-files=all", "--ignored=matching")
+	if after != "" {
+		t.Fatalf("init dirtied compressed checkout: %q", after)
+	}
+	result, err := fixture.refresh(t)
+	if err != nil {
+		t.Fatalf("refresh: %+v %v", result, err)
+	}
+}
+
+func initOrdinaryGitRepo(t *testing.T, ctx context.Context) string {
+	t.Helper()
+	repo := t.TempDir()
+	if err := runGit(ctx, repo, "init", "-b", "main"); err != nil {
+		t.Fatalf("git init: %v", err)
+	}
+	return repo
+}
+
+func assertOrdinaryGitWorktree(t *testing.T, ctx context.Context, repo, dbPath string) {
+	t.Helper()
+	root, portable, err := portableStoreRoot(ctx, dbPath)
+	if err != nil {
+		t.Fatalf("portable store root: %v", err)
+	}
+	if !portable || root != repo {
+		t.Fatalf("portable store root = %q, portable=%v, want ordinary worktree %q", root, portable, repo)
+	}
+}
+
+func assertInitializedLocalDatabase(t *testing.T, ctx context.Context, dbPath string) {
+	t.Helper()
+	st, err := store.OpenReadOnly(ctx, dbPath)
+	if err != nil {
+		t.Fatalf("open initialized database: %v", err)
+	}
+	if _, err := st.Status(ctx); err != nil {
+		t.Fatalf("read initialized database: %v", err)
+	}
+	if err := st.Close(); err != nil {
+		t.Fatalf("close initialized database: %v", err)
+	}
+}