diff --git a/README.md b/README.md
index eaadc58..2ade753 100644
--- a/README.md
+++ b/README.md
@@ -343,6 +343,8 @@ git gtr clean --merged --force --yes           # Force-clean and auto-confirm
 
 **Note:** The `--merged` mode auto-detects your hosting provider (GitHub or GitLab) from the `origin` remote URL and requires the corresponding CLI tool (`gh` or `glab`) to be installed and authenticated. For self-hosted instances, set the provider explicitly: `git gtr config set gtr.provider gitlab`.
 
+**Note:** `clean` also detects registry entries that are locked but whose directories no longer exist (for example, a crashed agent session that deleted its worktree directory). `git worktree prune` skips locked entries by design, so these linger and keep their branches checked out. `clean` offers to unlock and prune them; `--force` or `--yes` confirms automatically.
+
 ### `git gtr trust`
 
 Review and approve executable commands defined in the repository's `.gtrconfig` file. Hooks and editor/AI defaults from `.gtrconfig` are **not used** until explicitly trusted — this prevents malicious contributors from injecting arbitrary shell commands via shared config files.
diff --git a/lib/commands/clean.sh b/lib/commands/clean.sh
index a0226f8..ff3de22 100644
--- a/lib/commands/clean.sh
+++ b/lib/commands/clean.sh
@@ -67,6 +67,61 @@ _clean_should_skip() {
   return 1
 }
 
+# Recover registry entries that are locked but whose directories are gone
+# (e.g. an agent session crashed after its worktree directory was deleted).
+# `git worktree prune` skips locked entries by design, so they linger and
+# keep their branches checked out in a phantom worktree.
+# Usage: _clean_locked_phantoms repo_root yes_mode dry_run force
+_clean_locked_phantoms() {
+  local repo_root="$1" yes_mode="$2" dry_run="$3" force="${4:-0}"
+  local records
+  records=$(list_worktree_records "$repo_root")
+
+  local is_main="" dir="" wt_status="" line unlocked=0
+  while IFS= read -r line; do
+    case "$line" in
+      "")
+        if [ -n "$dir" ] && [ "$is_main" != "1" ] && [ "$wt_status" = "locked" ] && [ ! -e "$dir" ]; then
+          log_warn "Locked worktree entry with missing directory: $dir"
+          if [ "$dry_run" -eq 1 ]; then
+            log_info "[dry-run] Would unlock and prune: $dir"
+          elif [ "$force" -eq 1 ] || [ "$yes_mode" -eq 1 ] || \
+            prompt_yes_no "Unlock and prune '$dir'?"; then
+            if git -C "$repo_root" worktree unlock "$dir" 2>/dev/null; then
+              log_info "Unlocked missing worktree entry: $dir"
+              unlocked=$((unlocked + 1))
+            else
+              log_warn "Could not unlock worktree entry: $dir"
+            fi
+          else
+            log_info "Recover manually with: git worktree unlock '$dir' && git worktree prune"
+          fi
+        fi
+        is_main=""
+        dir=""
+        wt_status=""
+        ;;
+      "is_main "*)
+        is_main="${line#is_main }"
+        ;;
+      "path "*)
+        dir=$(_tsv_unescape_field "${line#path }")
+        ;;
+      "status "*)
+        wt_status="${line#status }"
+        ;;
+    esac
+  done <<EOF
+$records
+
+EOF
+
+  if [ "$unlocked" -gt 0 ]; then
+    git -C "$repo_root" worktree prune 2>/dev/null || true
+    log_info "Pruned $unlocked unlocked worktree entr$([ "$unlocked" -eq 1 ] && echo 'y' || echo 'ies')"
+  fi
+}
+
 # Remove worktrees whose PRs/MRs are merged (handles squash merges)
 # Usage: _clean_merged repo_root base_dir prefix yes_mode dry_run [force] [active_worktree_path] [target_ref]
 _clean_merged() {
@@ -206,6 +261,10 @@ cmd_clean() {
     active_worktree_path=$(canonicalize_path "$active_worktree_path" || printf "%s" "$active_worktree_path")
   fi
 
+  # Locked entries with missing directories survive `git worktree prune`;
+  # offer to unlock and prune them (may live outside base_dir)
+  _clean_locked_phantoms "$repo_root" "$yes_mode" "$dry_run" "$force"
+
   if [ ! -d "$base_dir" ]; then
     log_info "No worktrees directory to clean"
     return 0
diff --git a/lib/commands/help.sh b/lib/commands/help.sh
index 4a461b6..66657d3 100644
--- a/lib/commands/help.sh
+++ b/lib/commands/help.sh
@@ -311,6 +311,10 @@ Removes empty worktree directories and optionally removes worktrees whose
 PRs/MRs have been merged. Auto-detects GitHub (gh) or GitLab (glab) from
 the remote URL.
 
+Also detects registry entries that are locked but whose directories no
+longer exist (git worktree prune skips locked entries) and offers to
+unlock and prune them. Confirmed automatically with --force or --yes.
+
 Options:
   --merged            Also remove worktrees with merged PRs/MRs
   --to <ref>          Only remove worktrees for PRs/MRs merged into <ref>
diff --git a/tests/cmd_clean.bats b/tests/cmd_clean.bats
index 55d93f5..173d2bb 100644
--- a/tests/cmd_clean.bats
+++ b/tests/cmd_clean.bats
@@ -215,6 +215,77 @@ teardown() {
   [[ "$output" != *"dirty-not-merged"* ]]
 }
 
+# ── Locked entries with missing directories (#180) ──────────────────────────
+
+# Create a locked worktree whose directory has been deleted out from under git
+# Usage: create_locked_phantom <branch>
+create_locked_phantom() {
+  local branch="$1"
+  create_test_worktree "$branch"
+  git -C "$TEST_REPO" worktree lock "$TEST_WORKTREES_DIR/$branch"
+  rm -rf "$TEST_WORKTREES_DIR/$branch"
+}
+
+@test "cmd_clean surfaces recovery hint for locked missing worktree when declined" {
+  create_locked_phantom "phantom-hint"
+
+  run cmd_clean < /dev/null
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"Locked worktree entry with missing directory"* ]]
+  [[ "$output" == *"git worktree unlock"* ]]
+  # Entry stays registered without confirmation
+  git -C "$TEST_REPO" worktree list --porcelain | grep -q "phantom-hint"
+}
+
+@test "cmd_clean --force unlocks and prunes locked missing worktree" {
+  create_locked_phantom "phantom-force"
+
+  run cmd_clean --force
+  [ "$status" -eq 0 ]
+  ! git -C "$TEST_REPO" worktree list --porcelain | grep -q "phantom-force"
+  # Branch is no longer held by the phantom worktree
+  git -C "$TEST_REPO" branch -D phantom-force
+}
+
+@test "cmd_clean --yes unlocks and prunes locked missing worktree" {
+  create_locked_phantom "phantom-yes"
+
+  run cmd_clean --yes
+  [ "$status" -eq 0 ]
+  ! git -C "$TEST_REPO" worktree list --porcelain | grep -q "phantom-yes"
+}
+
+@test "cmd_clean --dry-run reports locked missing worktree without changes" {
+  create_locked_phantom "phantom-dry"
+
+  run cmd_clean --dry-run --force
+  [ "$status" -eq 0 ]
+  [[ "$output" == *"[dry-run] Would unlock and prune"* ]]
+  git -C "$TEST_REPO" worktree list --porcelain | grep -q "phantom-dry"
+}
+
+@test "cmd_clean --force keeps locked worktree whose directory exists" {
+  create_test_worktree "locked-alive"
+  git -C "$TEST_REPO" worktree lock "$TEST_WORKTREES_DIR/locked-alive"
+
+  run cmd_clean --force --yes
+  [ "$status" -eq 0 ]
+  [ -d "$TEST_WORKTREES_DIR/locked-alive" ]
+  git -C "$TEST_REPO" worktree list --porcelain | grep -q "locked-alive"
+}
+
+@test "cmd_clean --merged recovers locked missing worktree before merged pass" {
+  create_locked_phantom "phantom-merged"
+
+  _clean_detect_provider() { printf "github"; }
+  ensure_provider_cli() { return 0; }
+  check_branch_merged() { return 1; }
+
+  run cmd_clean --merged --force --yes
+  [ "$status" -eq 0 ]
+  ! git -C "$TEST_REPO" worktree list --porcelain | grep -q "phantom-merged"
+}
+
 @test "cmd_clean --merged --force skips the current active worktree" {
   create_test_worktree "active-merged"
   cd "$TEST_WORKTREES_DIR/active-merged" || false