diff --git a/src/context_engine/cli.py b/src/context_engine/cli.py
index d657bdb..970cd0b 100644
--- a/src/context_engine/cli.py
+++ b/src/context_engine/cli.py
@@ -1809,17 +1809,9 @@ def uninstall(yes: bool) -> None:
     lines.append(section(f"Uninstall · {project_name}"))
     lines.append("")
 
-    # Remove git hooks
-    hooks_dir = project_dir / ".git" / "hooks"
-    removed_hooks = 0
-    if hooks_dir.exists():
-        for hook_name in ["post-commit", "post-checkout", "post-merge"]:
-            hook_file = hooks_dir / hook_name
-            if hook_file.exists():
-                content = hook_file.read_text()
-                if "cce" in content.lower() or "context-engine" in content.lower():
-                    hook_file.unlink()
-                    removed_hooks += 1
+    # Remove git hooks (worktree-aware via git rev-parse --git-path).
+    from context_engine.indexer.git_hooks import uninstall_hooks
+    removed_hooks = uninstall_hooks(str(project_dir))
     if removed_hooks:
         lines.append(f"    {CROSS} {warn('Removed')} {removed_hooks} git hooks")
     else:
diff --git a/src/context_engine/indexer/git_hooks.py b/src/context_engine/indexer/git_hooks.py
index 1056668..9f6956e 100644
--- a/src/context_engine/indexer/git_hooks.py
+++ b/src/context_engine/indexer/git_hooks.py
@@ -1,6 +1,7 @@
 """Git hook installer and handler for triggering re-indexing."""
 import shutil
 import stat
+import subprocess
 import sys
 from pathlib import Path
 
@@ -8,6 +9,38 @@
 HOOK_NAMES = ["post-commit", "post-checkout", "post-merge"]
 
 
+def _resolve_hooks_dir(project_dir: str) -> Path | None:
+    """Return the directory git uses for hooks for `project_dir`, or None.
+
+    Why this is non-trivial: in a regular checkout, hooks live at
+    `<project>/.git/hooks/`. In a git worktree, `<project>/.git` is a *file*
+    pointing at `<main>/.git/worktrees/<name>/`, and hooks are shared with the
+    main repo at `<main>/.git/hooks/`. Hardcoding the regular-checkout layout
+    makes the installer silently no-op inside worktrees.
+
+    `git rev-parse --git-path hooks` resolves the right directory in both
+    cases (relative `.git/hooks` for regular checkouts, an absolute path to
+    the shared hooks dir for worktrees), and also respects `core.hooksPath`
+    if a project has overridden it.
+    """
+    try:
+        result = subprocess.run(
+            ["git", "rev-parse", "--git-path", "hooks"],
+            cwd=project_dir, capture_output=True, text=True, timeout=5,
+        )
+    except (FileNotFoundError, subprocess.TimeoutExpired):
+        return None
+    if result.returncode != 0:
+        return None
+    raw = result.stdout.strip()
+    if not raw:
+        return None
+    hooks_dir = Path(raw)
+    if not hooks_dir.is_absolute():
+        hooks_dir = Path(project_dir) / hooks_dir
+    return hooks_dir
+
+
 def _resolve_cce_binary() -> str:
     """Find an absolute path to the `cce` launcher.
 
@@ -38,9 +71,11 @@ def _hook_script() -> str:
 
 
 def install_hooks(project_dir: str) -> list[str]:
-    """Install CCE git hooks. Returns [] gracefully if not a git repo."""
-    hooks_dir = Path(project_dir) / ".git" / "hooks"
-    if not hooks_dir.exists():
+    """Install CCE git hooks. Returns [] gracefully if not a git repo or if
+    git is unavailable. Works correctly inside git worktrees, where hooks
+    live in the shared main-repo `.git/hooks` directory."""
+    hooks_dir = _resolve_hooks_dir(project_dir)
+    if hooks_dir is None or not hooks_dir.exists():
         return []
     installed = []
     for hook_name in HOOK_NAMES:
@@ -63,6 +98,37 @@ def _install_single_hook(hook_path: Path) -> None:
     hook_path.chmod(hook_path.stat().st_mode | stat.S_IEXEC)
 
 
+def uninstall_hooks(project_dir: str) -> int:
+    """Remove CCE-installed hook scripts from this project. Returns the number
+    of hook files actually removed. No-op outside a git repo or if git is
+    unavailable.
+
+    Detects \"CCE-installed\" by file content (presence of \"cce\" or
+    \"context-engine\") rather than the marker alone, so legacy installations
+    that pre-date HOOK_MARKER are still cleaned up. Worktree-aware via the
+    same `_resolve_hooks_dir` used by install.
+    """
+    hooks_dir = _resolve_hooks_dir(project_dir)
+    if hooks_dir is None or not hooks_dir.exists():
+        return 0
+    removed = 0
+    for hook_name in HOOK_NAMES:
+        hook_path = hooks_dir / hook_name
+        if not hook_path.exists():
+            continue
+        try:
+            content = hook_path.read_text()
+        except OSError:
+            continue
+        if "cce" in content.lower() or "context-engine" in content.lower():
+            try:
+                hook_path.unlink()
+                removed += 1
+            except OSError:
+                pass
+    return removed
+
+
 def get_changed_files_from_hook() -> list[str]:
     import subprocess
     try:
diff --git a/tests/indexer/test_git_hooks.py b/tests/indexer/test_git_hooks.py
index a1e2e87..2aaaaac 100644
--- a/tests/indexer/test_git_hooks.py
+++ b/tests/indexer/test_git_hooks.py
@@ -1,14 +1,64 @@
 import os
+import shutil
 import stat
+import subprocess
+
 import pytest
-from context_engine.indexer.git_hooks import install_hooks
+
+from context_engine.indexer.git_hooks import install_hooks, uninstall_hooks
+
+
+def _git(*args: str, cwd: str) -> str:
+    """Run git with config that doesn't require a real user/email — keeps the
+    tests usable on a fresh CI box where the user hasn't set git config."""
+    env = {
+        **os.environ,
+        "GIT_AUTHOR_NAME": "test", "GIT_AUTHOR_EMAIL": "t@t",
+        "GIT_COMMITTER_NAME": "test", "GIT_COMMITTER_EMAIL": "t@t",
+    }
+    return subprocess.run(
+        ["git", *args], cwd=cwd, env=env, check=True,
+        capture_output=True, text=True,
+    ).stdout
+
+
+def _git_available() -> bool:
+    return shutil.which("git") is not None
+
+
+pytestmark = pytest.mark.skipif(
+    not _git_available(),
+    reason="git binary not available — hook resolution requires real git",
+)
 
 
 @pytest.fixture
 def git_repo(tmp_path):
-    git_dir = tmp_path / ".git" / "hooks"
-    git_dir.mkdir(parents=True)
-    return tmp_path
+    """A real git repo at tmp_path. Avoids the previous fake-`.git/hooks/` dir
+    pattern, which silently masked the install logic — without `git init`,
+    `git rev-parse --git-path hooks` correctly refuses to claim the directory
+    is a repo and tests would not exercise the production path."""
+    proj = tmp_path / "proj"
+    proj.mkdir()
+    _git("init", "-b", "main", cwd=str(proj))
+    return proj
+
+
+@pytest.fixture
+def worktree(git_repo, tmp_path):
+    """A worktree of `git_repo` at tmp_path/wt-feat. Returns the worktree dir.
+
+    Worktrees share their hooks directory with the main repo's `.git/hooks/`
+    via the gitfile pointer in the worktree's `.git` (which is a *file*, not
+    a directory). Pinning install-from-worktree behavior here matches the
+    real-world setup that surfaced issue #48.
+    """
+    (git_repo / "file.txt").write_text("hi\n")
+    _git("add", "file.txt", cwd=str(git_repo))
+    _git("commit", "-m", "init", cwd=str(git_repo))
+    wt = tmp_path / "wt-feat"
+    _git("worktree", "add", "-b", "feat", str(wt), cwd=str(git_repo))
+    return wt
 
 
 def test_install_hooks_creates_post_commit(git_repo):
@@ -34,6 +84,7 @@ def test_install_hooks_creates_post_merge(git_repo):
 
 def test_install_hooks_preserves_existing(git_repo):
     existing_hook = git_repo / ".git" / "hooks" / "post-commit"
+    existing_hook.parent.mkdir(parents=True, exist_ok=True)
     existing_hook.write_text("#!/bin/sh\necho 'existing'\n")
     existing_hook.chmod(existing_hook.stat().st_mode | stat.S_IEXEC)
     install_hooks(project_dir=str(git_repo))
@@ -46,3 +97,66 @@ def test_install_hooks_returns_empty_for_non_git(tmp_path):
     """Non-git directory should return empty list, not raise."""
     result = install_hooks(project_dir=str(tmp_path))
     assert result == []
+
+
+def test_install_hooks_inside_worktree_writes_to_shared_hooks_dir(worktree, git_repo):
+    """Regression for issue #48: installing from inside a worktree previously
+    silently no-op'd because `<worktree>/.git` is a file, not a directory.
+    Hooks must land in the shared main-repo hooks dir, where they fire for
+    every worktree."""
+    installed = install_hooks(project_dir=str(worktree))
+    assert installed, "install returned [] — worktree path was not resolved"
+    shared_hook = git_repo / ".git" / "hooks" / "post-commit"
+    assert shared_hook.exists(), (
+        f"expected shared hook at {shared_hook}, got installed={installed}"
+    )
+    assert "cce hook" in shared_hook.read_text()
+    # The per-worktree gitdir does not get its own hooks/ — that's by design,
+    # git's behavior puts shared hooks in the main repo.
+    per_worktree = git_repo / ".git" / "worktrees" / "wt-feat" / "hooks"
+    if per_worktree.exists():
+        assert not (per_worktree / "post-commit").exists()
+
+
+def test_uninstall_hooks_removes_only_cce_hooks(git_repo):
+    """Uninstall scrubs CCE-installed hooks but keeps unrelated ones."""
+    install_hooks(project_dir=str(git_repo))
+    foreign = git_repo / ".git" / "hooks" / "pre-commit"  # not in HOOK_NAMES
+    foreign.write_text("#!/bin/sh\necho lint\n")
+    foreign.chmod(foreign.stat().st_mode | stat.S_IEXEC)
+
+    removed = uninstall_hooks(project_dir=str(git_repo))
+    assert removed == 3
+    assert not (git_repo / ".git" / "hooks" / "post-commit").exists()
+    # Foreign hook untouched.
+    assert foreign.exists()
+
+
+def test_uninstall_hooks_from_worktree_removes_shared_hooks(worktree, git_repo):
+    """Symmetry with install: uninstall run from a worktree must remove the
+    hooks the install path put in the shared dir, otherwise the user is left
+    with no way to clean up without cd'ing into the main checkout."""
+    install_hooks(project_dir=str(worktree))
+    shared_hook = git_repo / ".git" / "hooks" / "post-commit"
+    assert shared_hook.exists()
+
+    removed = uninstall_hooks(project_dir=str(worktree))
+    assert removed == 3
+    assert not shared_hook.exists()
+
+
+def test_uninstall_hooks_skips_non_cce_content(git_repo):
+    """A hand-rolled `post-commit` that has no CCE markers must be left alone.
+    Detection is content-based (presence of \"cce\" or \"context-engine\"), so
+    a user's pre-existing hook with neither token is preserved."""
+    other = git_repo / ".git" / "hooks" / "post-commit"
+    other.parent.mkdir(parents=True, exist_ok=True)
+    other.write_text("#!/bin/sh\necho 'unrelated'\n")
+    other.chmod(other.stat().st_mode | stat.S_IEXEC)
+    removed = uninstall_hooks(project_dir=str(git_repo))
+    assert removed == 0
+    assert other.exists()
+
+
+def test_uninstall_hooks_returns_zero_for_non_git(tmp_path):
+    assert uninstall_hooks(project_dir=str(tmp_path)) == 0