diff --git a/cmd/bd/init_stealth.go b/cmd/bd/init_stealth.go
index ece57b6e..d9e71ee8 100644
--- a/cmd/bd/init_stealth.go
+++ b/cmd/bd/init_stealth.go
@@ -41,8 +41,9 @@ func setupStealthMode(verbose bool) error {
 // This is the correct approach for per-repository user-specific ignores (GitHub #704).
 // Unlike global gitignore, patterns here are relative to the repo root.
 func setupGitExclude(verbose bool) error {
-	// Find the .git directory (handles both regular repos and worktrees)
-	gitDir, err := exec.Command("git", "rev-parse", "--git-dir").Output()
+	// Find the common .git directory (handles worktrees correctly - GH#1053)
+	// Use --git-common-dir to get the main repo's .git, not the worktree's .git/worktrees/<name>
+	gitDir, err := exec.Command("git", "rev-parse", "--git-common-dir").Output()
 	if err != nil {
 		return fmt.Errorf("not a git repository")
 	}
@@ -113,7 +114,8 @@ func setupGitExclude(verbose bool) error {
 // This is separate from stealth mode - fork protection is specifically about
 // preventing beads/Claude files from appearing in upstream PRs.
 func setupForkExclude(verbose bool) error {
-	gitDir, err := exec.Command("git", "rev-parse", "--git-dir").Output()
+	// Use --git-common-dir to get main repo's .git, not worktree's (GH#1053)
+	gitDir, err := exec.Command("git", "rev-parse", "--git-common-dir").Output()
 	if err != nil {
 		return fmt.Errorf("not a git repository")
 	}
diff --git a/cmd/bd/init_stealth_test.go b/cmd/bd/init_stealth_test.go
new file mode 100644
index 00000000..fd3c3093
--- /dev/null
+++ b/cmd/bd/init_stealth_test.go
@@ -0,0 +1,208 @@
+package main
+
+import (
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+// TestSetupGitExclude_Worktree verifies that setupGitExclude writes to the main
+// repo's .git/info/exclude, not the worktree's .git/worktrees/<name>/info/exclude.
+// This is the fix for GH#1053.
+func TestSetupGitExclude_Worktree(t *testing.T) {
+	// Create main repo
+	mainDir := t.TempDir()
+	cmd := exec.Command("git", "init", "--initial-branch=main")
+	cmd.Dir = mainDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init main repo: %v", err)
+	}
+
+	// Configure git user
+	for _, args := range [][]string{
+		{"git", "config", "user.email", "test@test.com"},
+		{"git", "config", "user.name", "Test User"},
+	} {
+		cmd := exec.Command(args[0], args[1:]...)
+		cmd.Dir = mainDir
+		_ = cmd.Run()
+	}
+
+	// Create initial commit (required for worktree)
+	dummyFile := filepath.Join(mainDir, "README.md")
+	if err := os.WriteFile(dummyFile, []byte("# Test\n"), 0644); err != nil {
+		t.Fatalf("failed to create dummy file: %v", err)
+	}
+	cmd = exec.Command("git", "add", ".")
+	cmd.Dir = mainDir
+	_ = cmd.Run()
+	cmd = exec.Command("git", "commit", "-m", "initial")
+	cmd.Dir = mainDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to create initial commit: %v", err)
+	}
+
+	// Create worktree
+	worktreeDir := filepath.Join(t.TempDir(), "worktree")
+	cmd = exec.Command("git", "worktree", "add", worktreeDir, "-b", "feature")
+	cmd.Dir = mainDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to create worktree: %v", err)
+	}
+
+	// Change to worktree directory and run setupGitExclude
+	origDir, _ := os.Getwd()
+	if err := os.Chdir(worktreeDir); err != nil {
+		t.Fatalf("failed to chdir to worktree: %v", err)
+	}
+	defer os.Chdir(origDir)
+
+	if err := setupGitExclude(false); err != nil {
+		t.Fatalf("setupGitExclude failed: %v", err)
+	}
+
+	// Verify: main repo's .git/info/exclude should have the patterns
+	mainExcludePath := filepath.Join(mainDir, ".git", "info", "exclude")
+	content, err := os.ReadFile(mainExcludePath)
+	if err != nil {
+		t.Fatalf("failed to read main exclude file: %v", err)
+	}
+
+	if !strings.Contains(string(content), ".beads/") {
+		t.Errorf("main repo exclude missing .beads/ pattern: %s", content)
+	}
+	if !strings.Contains(string(content), ".claude/settings.local.json") {
+		t.Errorf("main repo exclude missing .claude/settings.local.json pattern: %s", content)
+	}
+
+	// Verify: worktree's .git/worktrees/<name>/info/exclude should NOT exist
+	// (or should not have the patterns if it exists)
+	worktreeGitDir, err := exec.Command("git", "-C", worktreeDir, "rev-parse", "--git-dir").Output()
+	if err != nil {
+		t.Fatalf("failed to get worktree git dir: %v", err)
+	}
+	worktreeExcludePath := filepath.Join(strings.TrimSpace(string(worktreeGitDir)), "info", "exclude")
+	if worktreeContent, err := os.ReadFile(worktreeExcludePath); err == nil {
+		// If worktree exclude file exists, it should NOT have the beads patterns
+		if strings.Contains(string(worktreeContent), ".beads/") {
+			t.Errorf("worktree exclude should not have .beads/ pattern (it was written to wrong location)")
+		}
+	}
+	// If the file doesn't exist, that's fine - we didn't create it
+}
+
+// TestSetupForkExclude_Worktree verifies that setupForkExclude writes to the main
+// repo's .git/info/exclude, not the worktree's path. This is part of GH#1053.
+func TestSetupForkExclude_Worktree(t *testing.T) {
+	// Create main repo
+	mainDir := t.TempDir()
+	cmd := exec.Command("git", "init", "--initial-branch=main")
+	cmd.Dir = mainDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init main repo: %v", err)
+	}
+
+	// Configure git user
+	for _, args := range [][]string{
+		{"git", "config", "user.email", "test@test.com"},
+		{"git", "config", "user.name", "Test User"},
+	} {
+		cmd := exec.Command(args[0], args[1:]...)
+		cmd.Dir = mainDir
+		_ = cmd.Run()
+	}
+
+	// Create initial commit (required for worktree)
+	dummyFile := filepath.Join(mainDir, "README.md")
+	if err := os.WriteFile(dummyFile, []byte("# Test\n"), 0644); err != nil {
+		t.Fatalf("failed to create dummy file: %v", err)
+	}
+	cmd = exec.Command("git", "add", ".")
+	cmd.Dir = mainDir
+	_ = cmd.Run()
+	cmd = exec.Command("git", "commit", "-m", "initial")
+	cmd.Dir = mainDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to create initial commit: %v", err)
+	}
+
+	// Create worktree
+	worktreeDir := filepath.Join(t.TempDir(), "worktree")
+	cmd = exec.Command("git", "worktree", "add", worktreeDir, "-b", "feature")
+	cmd.Dir = mainDir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to create worktree: %v", err)
+	}
+
+	// Change to worktree directory and run setupForkExclude
+	origDir, _ := os.Getwd()
+	if err := os.Chdir(worktreeDir); err != nil {
+		t.Fatalf("failed to chdir to worktree: %v", err)
+	}
+	defer os.Chdir(origDir)
+
+	if err := setupForkExclude(false); err != nil {
+		t.Fatalf("setupForkExclude failed: %v", err)
+	}
+
+	// Verify: main repo's .git/info/exclude should have the patterns
+	mainExcludePath := filepath.Join(mainDir, ".git", "info", "exclude")
+	content, err := os.ReadFile(mainExcludePath)
+	if err != nil {
+		t.Fatalf("failed to read main exclude file: %v", err)
+	}
+
+	if !strings.Contains(string(content), ".beads/") {
+		t.Errorf("main repo exclude missing .beads/ pattern: %s", content)
+	}
+
+	// Verify: worktree's .git/worktrees/<name>/info/exclude should NOT exist
+	// (or should not have the patterns if it exists)
+	worktreeGitDir, err := exec.Command("git", "-C", worktreeDir, "rev-parse", "--git-dir").Output()
+	if err != nil {
+		t.Fatalf("failed to get worktree git dir: %v", err)
+	}
+	worktreeExcludePath := filepath.Join(strings.TrimSpace(string(worktreeGitDir)), "info", "exclude")
+	if worktreeContent, err := os.ReadFile(worktreeExcludePath); err == nil {
+		// If worktree exclude file exists, it should NOT have the beads patterns
+		if strings.Contains(string(worktreeContent), ".beads/") {
+			t.Errorf("worktree exclude should not have .beads/ pattern (it was written to wrong location)")
+		}
+	}
+}
+
+// TestSetupGitExclude_RegularRepo verifies that setupGitExclude still works
+// correctly in a regular (non-worktree) repo.
+func TestSetupGitExclude_RegularRepo(t *testing.T) {
+	dir := t.TempDir()
+	cmd := exec.Command("git", "init", "--initial-branch=main")
+	cmd.Dir = dir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	origDir, _ := os.Getwd()
+	if err := os.Chdir(dir); err != nil {
+		t.Fatalf("failed to chdir: %v", err)
+	}
+	defer os.Chdir(origDir)
+
+	if err := setupGitExclude(false); err != nil {
+		t.Fatalf("setupGitExclude failed: %v", err)
+	}
+
+	excludePath := filepath.Join(dir, ".git", "info", "exclude")
+	content, err := os.ReadFile(excludePath)
+	if err != nil {
+		t.Fatalf("failed to read exclude file: %v", err)
+	}
+
+	if !strings.Contains(string(content), ".beads/") {
+		t.Errorf("exclude file missing .beads/ pattern: %s", content)
+	}
+	if !strings.Contains(string(content), ".claude/settings.local.json") {
+		t.Errorf("exclude file missing .claude/settings.local.json pattern: %s", content)
+	}
+}