diff --git a/internal/sandbox/profile.go b/internal/sandbox/profile.go
index 915bb92be..4ab3dcaa7 100644
--- a/internal/sandbox/profile.go
+++ b/internal/sandbox/profile.go
@@ -63,10 +63,72 @@ var sandboxFullyProtectedMetadataNames = []string{".zero", ".agents"}
 // subprocesses. Nonexistent paths are harmless no-ops in every backend's
 // enforcement (seatbelt regex, bwrap ro-bind, Windows ACL deny entry).
 func gitMetadataWriteCarveouts(root string) []string {
+	// Worktrees/submodules store .git as a *file* ("gitdir: <path>"), so
+	// .git/hooks has no parent dir — a --tmpfs carveout there makes bwrap fail
+	// ("Can't mkdir parents ... Not a directory") and blocks every sandboxed
+	// tool. Resolve the real (common) git dir in that case; otherwise keep the
+	// plain-checkout paths (harmless no-ops when .git is absent).
+	gitDir := filepath.Join(root, ".git")
+	if info, err := os.Stat(gitDir); err == nil && !info.IsDir() {
+		if real := resolveGitDir(root); real != "" {
+			gitDir = resolveGitCommonDir(real)
+		}
+	}
 	return []string{
-		filepath.Join(root, ".git", "hooks"),
-		filepath.Join(root, ".git", "config"),
+		filepath.Join(gitDir, "hooks"),
+		filepath.Join(gitDir, "config"),
+	}
+}
+
+// resolveGitDir returns the real git directory for a workspace root, handling
+// both regular checkouts (.git is a directory) and worktrees/submodules (.git
+// is a file containing "gitdir: <path>"). Returns "" when .git is absent, so
+// carveouts collapse to no-ops instead of pointing at a bogus path — a bogus
+// path under a .git *file* makes bwrap fail ("Can't mkdir parents ... Not a
+// directory") and blocks every sandboxed tool.
+func resolveGitDir(root string) string {
+	gitPath := filepath.Join(root, ".git")
+	info, err := os.Stat(gitPath)
+	if err != nil {
+		return ""
+	}
+	if info.IsDir() {
+		return gitPath
+	}
+	data, err := os.ReadFile(gitPath)
+	if err != nil {
+		return ""
+	}
+	dir := strings.TrimSpace(strings.TrimPrefix(strings.TrimSpace(string(data)), "gitdir:"))
+	if dir == "" {
+		return ""
+	}
+	// Worktree gitdir pointers are often relative to the worktree root.
+	if !filepath.IsAbs(dir) {
+		dir = filepath.Join(root, dir)
+	}
+	if _, err := os.Stat(dir); err != nil {
+		return ""
+	}
+	return dir
+}
+
+// resolveGitCommonDir returns the shared git dir for a (possibly worktree)
+// gitDir. Worktree gitdirs carry a "commondir" pointer (usually "../.."); plain
+// checkouts have none and are their own common dir.
+func resolveGitCommonDir(gitDir string) string {
+	data, err := os.ReadFile(filepath.Join(gitDir, "commondir"))
+	if err != nil {
+		return gitDir
+	}
+	common := strings.TrimSpace(string(data))
+	if common == "" {
+		return gitDir
+	}
+	if !filepath.IsAbs(common) {
+		common = filepath.Join(gitDir, common)
 	}
+	return filepath.Clean(common)
 }
 
 func DefaultPermissionProfile(workspaceRoot string) PermissionProfile {
diff --git a/internal/sandbox/profile_worktree_test.go b/internal/sandbox/profile_worktree_test.go
new file mode 100644
index 000000000..f67fecf32
--- /dev/null
+++ b/internal/sandbox/profile_worktree_test.go
@@ -0,0 +1,75 @@
+package sandbox
+
+import (
+	"os"
+	"path/filepath"
+	"testing"
+)
+
+// Worktree/submodule checkouts store .git as a *file* ("gitdir: <path>"). The
+// hooks/config carveout must resolve the real (common) git dir instead of the
+// bogus <root>/.git/hooks under that file — a --tmpfs there makes bwrap fail
+// ("Can't mkdir parents ... Not a directory") and blocks every sandboxed tool.
+func TestGitMetadataWriteCarveoutsResolvesWorktree(t *testing.T) {
+	main := t.TempDir()
+	commonGit := filepath.Join(main, ".git")
+	worktreeGit := filepath.Join(commonGit, "worktrees", "wt")
+	if err := os.MkdirAll(worktreeGit, 0o755); err != nil {
+		t.Fatal(err)
+	}
+	if err := os.WriteFile(filepath.Join(worktreeGit, "commondir"), []byte("../..\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	worktree := t.TempDir()
+	if err := os.WriteFile(filepath.Join(worktree, ".git"), []byte("gitdir: "+worktreeGit+"\n"), 0o644); err != nil {
+		t.Fatal(err)
+	}
+
+	got := gitMetadataWriteCarveouts(worktree)
+	want := []string{
+		filepath.Join(commonGit, "hooks"),
+		filepath.Join(commonGit, "config"),
+	}
+	if len(got) != len(want) {
+		t.Fatalf("carveouts = %v, want %v", got, want)
+	}
+	for i := range want {
+		if got[i] != want[i] {
+			t.Fatalf("carveout[%d] = %q, want %q", i, got[i], want[i])
+		}
+	}
+	// Must never point under the .git *file* — that path has no mkdir-able parent.
+	bogus := filepath.Join(worktree, ".git", "hooks")
+	for _, c := range got {
+		if c == bogus {
+			t.Fatalf("carveout points under .git file: %q", c)
+		}
+	}
+}
+
+// Plain checkouts (.git is a dir) and .git-absent roots keep the literal
+// <root>/.git/{hooks,config} carveouts.
+func TestGitMetadataWriteCarveoutsPlainCheckout(t *testing.T) {
+	root := t.TempDir()
+	want := []string{
+		filepath.Join(root, ".git", "hooks"),
+		filepath.Join(root, ".git", "config"),
+	}
+	got := gitMetadataWriteCarveouts(root)
+	for i := range want {
+		if got[i] != want[i] {
+			t.Fatalf("carveout[%d] = %q, want %q", i, got[i], want[i])
+		}
+	}
+
+	if err := os.MkdirAll(filepath.Join(root, ".git"), 0o755); err != nil {
+		t.Fatal(err)
+	}
+	got = gitMetadataWriteCarveouts(root)
+	for i := range want {
+		if got[i] != want[i] {
+			t.Fatalf("dir carveout[%d] = %q, want %q", i, got[i], want[i])
+		}
+	}
+}