diff --git a/README.md b/README.md
index d1a7ff4..c38e391 100644
--- a/README.md
+++ b/README.md
@@ -325,6 +325,7 @@ Remove worktrees: clean up empty directories, or remove those with merged PRs/MR
 ```bash
 git gtr clean                                  # Remove empty worktree directories and prune
 git gtr clean --merged                         # Remove worktrees for merged PRs/MRs
+git gtr clean --merged --to main               # Only remove worktrees merged to main
 git gtr clean --merged --dry-run               # Preview which worktrees would be removed
 git gtr clean --merged --yes                   # Remove without confirmation prompts
 git gtr clean --merged --force                 # Force-clean merged, ignoring local changes
@@ -334,6 +335,7 @@ git gtr clean --merged --force --yes           # Force-clean and auto-confirm
 **Options:**
 
 - `--merged`: Remove worktrees whose branches have merged PRs/MRs (also deletes the branch)
+- `--to <ref>`: Limit `--merged` cleanup to PRs/MRs merged into the given base ref
 - `--dry-run`, `-n`: Preview changes without removing
 - `--yes`, `-y`: Non-interactive mode (skip confirmation prompts)
 - `--force`, `-f`: Force removal even if worktree has uncommitted changes or untracked files
diff --git a/completions/_git-gtr b/completions/_git-gtr
index e0a5ba3..676338a 100644
--- a/completions/_git-gtr
+++ b/completions/_git-gtr
@@ -80,6 +80,7 @@ _git-gtr() {
   if (( CURRENT >= 4 )) && [[ $words[3] == clean ]]; then
     _arguments \
       '--merged[Remove worktrees with merged PRs/MRs]' \
+      '--to[Only remove worktrees for PRs/MRs merged into this ref]:ref:' \
       '--yes[Skip confirmation prompts]' \
       '-y[Skip confirmation prompts]' \
       '--dry-run[Show what would be removed]' \
diff --git a/completions/git-gtr.fish b/completions/git-gtr.fish
index 7fdc786..ca7e8f8 100644
--- a/completions/git-gtr.fish
+++ b/completions/git-gtr.fish
@@ -99,6 +99,7 @@ complete -c git -n '__fish_git_gtr_using_command ai' -l ai -d 'AI tool to use' -
 
 # Clean command options
 complete -c git -n '__fish_git_gtr_using_command clean' -l merged -d 'Remove worktrees with merged PRs/MRs'
+complete -c git -n '__fish_git_gtr_using_command clean' -l to -d 'Only remove worktrees for PRs/MRs merged into this ref' -r
 complete -c git -n '__fish_git_gtr_using_command clean' -l yes -d 'Skip confirmation prompts'
 complete -c git -n '__fish_git_gtr_using_command clean' -s y -d 'Skip confirmation prompts'
 complete -c git -n '__fish_git_gtr_using_command clean' -l dry-run -d 'Show what would be removed'
diff --git a/completions/gtr.bash b/completions/gtr.bash
index 13314cf..8bcba08 100644
--- a/completions/gtr.bash
+++ b/completions/gtr.bash
@@ -82,7 +82,7 @@ _git_gtr() {
       ;;
     clean)
       if [[ "$cur" == -* ]]; then
-        COMPREPLY=($(compgen -W "--merged --yes -y --dry-run -n --force -f" -- "$cur"))
+        COMPREPLY=($(compgen -W "--merged --to --yes -y --dry-run -n --force -f" -- "$cur"))
       fi
       ;;
     copy)
diff --git a/lib/commands/clean.sh b/lib/commands/clean.sh
index 477d07d..2c3c1b1 100644
--- a/lib/commands/clean.sh
+++ b/lib/commands/clean.sh
@@ -68,9 +68,9 @@ _clean_should_skip() {
 }
 
 # 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]
+# Usage: _clean_merged repo_root base_dir prefix yes_mode dry_run [force] [active_worktree_path] [target_ref]
 _clean_merged() {
-  local repo_root="$1" base_dir="$2" prefix="$3" yes_mode="$4" dry_run="$5" force="${6:-0}" active_worktree_path="${7:-}"
+  local repo_root="$1" base_dir="$2" prefix="$3" yes_mode="$4" dry_run="$5" force="${6:-0}" active_worktree_path="${7:-}" target_ref="${8:-}"
 
   log_step "Checking for worktrees with merged PRs/MRs..."
 
@@ -90,17 +90,19 @@ _clean_merged() {
 
     local branch
     branch=$(current_branch "$dir") || true
+    local branch_tip
+    branch_tip=$(git -C "$dir" rev-parse HEAD 2>/dev/null || true)
 
     # Skip main repo branch silently (not counted)
     [ "$branch" = "$main_branch" ] && continue
 
-    if _clean_should_skip "$dir" "$branch" "$force" "$active_worktree_path"; then
-      skipped=$((skipped + 1))
-      continue
-    fi
-
     # Check if branch has a merged PR/MR
-    if check_branch_merged "$provider" "$branch"; then
+    if check_branch_merged "$provider" "$branch" "$target_ref" "$branch_tip"; then
+      if _clean_should_skip "$dir" "$branch" "$force" "$active_worktree_path"; then
+        skipped=$((skipped + 1))
+        continue
+      fi
+
       if [ "$dry_run" -eq 1 ]; then
         log_info "[dry-run] Would remove: $branch ($dir)"
         removed=$((removed + 1))
@@ -146,17 +148,24 @@ _clean_merged() {
 cmd_clean() {
   local _spec
   _spec="--merged
+--to: value
 --yes|-y
 --dry-run|-n
 --force|-f"
   parse_args "$_spec" "$@"
 
   local merged_mode="${_arg_merged:-0}"
+  local target_ref="${_arg_to:-}"
   local yes_mode="${_arg_yes:-0}"
   local dry_run="${_arg_dry_run:-0}"
   local force="${_arg_force:-0}"
   local active_worktree_path=""
 
+  if [ -n "$target_ref" ] && [ "$merged_mode" -ne 1 ]; then
+    log_error "--to can only be used with --merged"
+    return 1
+  fi
+
   log_step "Cleaning up stale worktrees..."
 
   # Run git worktree prune
@@ -204,6 +213,6 @@ EOF
 
   # --merged mode: remove worktrees with merged PRs/MRs (handles squash merges)
   if [ "$merged_mode" -eq 1 ]; then
-    _clean_merged "$repo_root" "$base_dir" "$prefix" "$yes_mode" "$dry_run" "$force" "$active_worktree_path"
+    _clean_merged "$repo_root" "$base_dir" "$prefix" "$yes_mode" "$dry_run" "$force" "$active_worktree_path" "$target_ref"
   fi
 }
diff --git a/lib/commands/help.sh b/lib/commands/help.sh
index c680987..1c99694 100644
--- a/lib/commands/help.sh
+++ b/lib/commands/help.sh
@@ -303,6 +303,7 @@ the remote URL.
 
 Options:
   --merged            Also remove worktrees with merged PRs/MRs
+  --to <ref>          Only remove worktrees for PRs/MRs merged into <ref>
   --yes, -y           Skip confirmation prompts
   --dry-run, -n       Show what would be removed without removing
   --force, -f         Force removal even if worktree has uncommitted changes or untracked files
@@ -310,6 +311,7 @@ Options:
 Examples:
   git gtr clean                                 # Clean empty directories
   git gtr clean --merged                        # Also clean merged PRs
+  git gtr clean --merged --to main              # Only clean PRs merged to main
   git gtr clean --merged --dry-run              # Preview merged cleanup
   git gtr clean --merged --yes                  # Auto-confirm everything
   git gtr clean --merged --force                # Force-clean merged, ignoring local changes
@@ -566,6 +568,7 @@ SETUP & MAINTENANCE:
   clean [options]
          Remove stale/prunable worktrees and empty directories
          --merged: also remove worktrees with merged PRs/MRs
+         --to <ref>: limit merged cleanup to PRs/MRs merged into <ref>
                    Auto-detects GitHub (gh) or GitLab (glab) from remote URL
                    Override: git gtr config set gtr.provider gitlab
          --yes, -y: skip confirmation prompts
diff --git a/lib/provider.sh b/lib/provider.sh
index e28cdf3..53d5be3 100755
--- a/lib/provider.sh
+++ b/lib/provider.sh
@@ -97,23 +97,96 @@ ensure_provider_cli() {
   esac
 }
 
-# Check if a branch has a merged PR/MR on the detected provider
-# Usage: check_branch_merged <provider> <branch>
+# Normalize user-provided refs to plain branch names for provider filters.
+# Usage: normalize_target_ref [target_ref]
+normalize_target_ref() {
+  local target_ref="${1:-}"
+  local remote_ref
+
+  [ -n "$target_ref" ] || return 0
+
+  case "$target_ref" in
+    refs/heads/*)
+      printf "%s" "${target_ref#refs/heads/}"
+      ;;
+    refs/remotes/*)
+      remote_ref="${target_ref#refs/remotes/}"
+      printf "%s" "${remote_ref#*/}"
+      ;;
+    origin/*|upstream/*)
+      printf "%s" "${target_ref#*/}"
+      ;;
+    *)
+      if git show-ref --verify --quiet "refs/remotes/$target_ref" 2>/dev/null; then
+        printf "%s" "${target_ref#*/}"
+      else
+        printf "%s" "$target_ref"
+      fi
+      ;;
+  esac
+}
+
+# Check if a branch has a merged PR/MR on the detected provider.
+# When branch_tip is provided, require the merged PR/MR to point at the same
+# commit so reused branch names do not match older merged PRs.
+# Usage: check_branch_merged <provider> <branch> [target_ref] [branch_tip]
 # Returns 0 if merged, 1 if not
 check_branch_merged() {
   local provider="$1"
   local branch="$2"
+  local target_ref="${3:-}"
+  local branch_tip="${4:-}"
+  local normalized_target_ref
+
+  normalized_target_ref=$(normalize_target_ref "$target_ref") || true
 
   case "$provider" in
     github)
-      local pr_state
-      pr_state=$(gh pr list --head "$branch" --state merged --json state --jq '.[0].state' 2>/dev/null || true)
-      [ "$pr_state" = "MERGED" ]
+      local -a gh_args
+      local pr_matches
+      gh_args=(pr list --head "$branch" --state merged --limit 1000)
+      if [ -n "$normalized_target_ref" ]; then
+        gh_args+=(--base "$normalized_target_ref")
+      fi
+      if [ -n "$normalized_target_ref" ]; then
+        if [ -n "$branch_tip" ]; then
+          pr_matches=$(gh "${gh_args[@]}" --json state,headRefOid --jq "map(select(.state == \"MERGED\" and .headRefOid == \"$branch_tip\")) | length" 2>/dev/null || true)
+        else
+          pr_matches=$(gh "${gh_args[@]}" --json state --jq 'map(select(.state == "MERGED")) | length' 2>/dev/null || true)
+        fi
+      else
+        if [ -n "$branch_tip" ]; then
+          pr_matches=$(gh "${gh_args[@]}" --json state,headRefOid --jq "map(select(.state == \"MERGED\" and .headRefOid == \"$branch_tip\")) | length" 2>/dev/null || true)
+        else
+          pr_matches=$(gh "${gh_args[@]}" --json state --jq 'map(select(.state == "MERGED")) | length' 2>/dev/null || true)
+        fi
+      fi
+      [ "${pr_matches:-0}" -gt 0 ]
       ;;
     gitlab)
-      local mr_result
-      mr_result=$(glab mr list --source-branch "$branch" --merged --per-page 1 --output json 2>/dev/null || true)
-      [ -n "$mr_result" ] && [ "$mr_result" != "[]" ] && [ "$mr_result" != "null" ]
+      local mr_result compact_result
+      local -a glab_args
+      glab_args=(mr list --source-branch "$branch" --merged --all --output json)
+      if [ -n "$normalized_target_ref" ]; then
+        glab_args+=(--target-branch "$normalized_target_ref")
+      fi
+
+      mr_result=$(glab "${glab_args[@]}" 2>/dev/null || true)
+      [ -n "$mr_result" ] && [ "$mr_result" != "[]" ] && [ "$mr_result" != "null" ] || return 1
+
+      if [ -n "$branch_tip" ]; then
+        compact_result=$(printf "%s" "$mr_result" | tr -d '[:space:]')
+        case "$compact_result" in
+          *"\"sha\":\"$branch_tip\""*|*"\"head_sha\":\"$branch_tip\""*)
+            return 0
+            ;;
+          *)
+            return 1
+            ;;
+        esac
+      fi
+
+      return 0
       ;;
     *)
       return 1
diff --git a/scripts/generate-completions.sh b/scripts/generate-completions.sh
index 1072645..d99d41d 100755
--- a/scripts/generate-completions.sh
+++ b/scripts/generate-completions.sh
@@ -176,7 +176,7 @@ MIDDLE1
       ;;
     clean)
       if [[ "$cur" == -* ]]; then
-        COMPREPLY=($(compgen -W "--merged --yes -y --dry-run -n --force -f" -- "$cur"))
+        COMPREPLY=($(compgen -W "--merged --to --yes -y --dry-run -n --force -f" -- "$cur"))
       fi
       ;;
     copy)
@@ -339,6 +339,7 @@ _git-gtr() {
   if (( CURRENT >= 4 )) && [[ $words[3] == clean ]]; then
     _arguments \
       '--merged[Remove worktrees with merged PRs/MRs]' \
+      '--to[Only remove worktrees for PRs/MRs merged into this ref]:ref:' \
       '--yes[Skip confirmation prompts]' \
       '-y[Skip confirmation prompts]' \
       '--dry-run[Show what would be removed]' \
@@ -578,6 +579,7 @@ MIDDLE1
 
 # Clean command options
 complete -c git -n '__fish_git_gtr_using_command clean' -l merged -d 'Remove worktrees with merged PRs/MRs'
+complete -c git -n '__fish_git_gtr_using_command clean' -l to -d 'Only remove worktrees for PRs/MRs merged into this ref' -r
 complete -c git -n '__fish_git_gtr_using_command clean' -l yes -d 'Skip confirmation prompts'
 complete -c git -n '__fish_git_gtr_using_command clean' -s y -d 'Skip confirmation prompts'
 complete -c git -n '__fish_git_gtr_using_command clean' -l dry-run -d 'Show what would be removed'
diff --git a/tests/cmd_clean.bats b/tests/cmd_clean.bats
index 59160c2..5b8ef5b 100644
--- a/tests/cmd_clean.bats
+++ b/tests/cmd_clean.bats
@@ -123,6 +123,12 @@ teardown() {
   [ "$status" -eq 0 ]
 }
 
+@test "cmd_clean rejects --to without --merged" {
+  run cmd_clean --to main
+  [ "$status" -eq 1 ]
+  [[ "$output" == *"--to can only be used with --merged"* ]]
+}
+
 @test "cmd_clean --merged --force removes dirty merged worktrees" {
   create_test_worktree "merged-force"
   echo "dirty" > "$TEST_WORKTREES_DIR/merged-force/dirty.txt"
@@ -130,7 +136,7 @@ teardown() {
 
   _clean_detect_provider() { printf "github"; }
   ensure_provider_cli() { return 0; }
-  check_branch_merged() { [ "$2" = "merged-force" ]; }
+  check_branch_merged() { [ "$2" = "merged-force" ] && [ -z "$3" ]; }
   run_hooks_in() { return 0; }
   run_hooks() { return 0; }
 
@@ -139,6 +145,54 @@ teardown() {
   [ ! -d "$TEST_WORKTREES_DIR/merged-force" ]
 }
 
+@test "cmd_clean --merged --to filters by target ref" {
+  create_test_worktree "merged-to-main"
+  create_test_worktree "merged-to-feature"
+
+  _clean_detect_provider() { printf "github"; }
+  ensure_provider_cli() { return 0; }
+  check_branch_merged() {
+    [ "$3" = "main" ] && [ "$2" = "merged-to-main" ]
+  }
+  run_hooks_in() { return 0; }
+  run_hooks() { return 0; }
+
+  run cmd_clean --merged --to main --yes
+  [ "$status" -eq 0 ]
+  [ ! -d "$TEST_WORKTREES_DIR/merged-to-main" ]
+  [ -d "$TEST_WORKTREES_DIR/merged-to-feature" ]
+}
+
+@test "cmd_clean passes current branch HEAD to merged check" {
+  create_test_worktree "merged-tip"
+  local branch_tip
+  branch_tip=$(git -C "$TEST_WORKTREES_DIR/merged-tip" rev-parse HEAD)
+
+  _clean_detect_provider() { printf "github"; }
+  ensure_provider_cli() { return 0; }
+  check_branch_merged() { [ "$2" = "merged-tip" ] && [ "$3" = "main" ] && [ "$4" = "$branch_tip" ]; }
+  run_hooks_in() { return 0; }
+  run_hooks() { return 0; }
+
+  run cmd_clean --merged --to main --yes
+  [ "$status" -eq 0 ]
+  [ ! -d "$TEST_WORKTREES_DIR/merged-tip" ]
+}
+
+@test "cmd_clean does not log dirty skip for non-merged worktree" {
+  create_test_worktree "dirty-not-merged"
+  echo "dirty" > "$TEST_WORKTREES_DIR/dirty-not-merged/dirty.txt"
+  git -C "$TEST_WORKTREES_DIR/dirty-not-merged" add dirty.txt
+
+  _clean_detect_provider() { printf "github"; }
+  ensure_provider_cli() { return 0; }
+  check_branch_merged() { return 1; }
+
+  run cmd_clean --merged --to main --yes
+  [ "$status" -eq 0 ]
+  [[ "$output" != *"dirty-not-merged"* ]]
+}
+
 @test "cmd_clean --merged --force skips the current active worktree" {
   create_test_worktree "active-merged"
   cd "$TEST_WORKTREES_DIR/active-merged" || false
@@ -147,7 +201,7 @@ teardown() {
 
   _clean_detect_provider() { printf "github"; }
   ensure_provider_cli() { return 0; }
-  check_branch_merged() { [ "$2" = "active-merged" ]; }
+  check_branch_merged() { [ "$2" = "active-merged" ] && [ -z "$3" ]; }
   run_hooks_in() { return 0; }
   run_hooks() { return 0; }
 
diff --git a/tests/cmd_help.bats b/tests/cmd_help.bats
index 274f015..8b23f42 100644
--- a/tests/cmd_help.bats
+++ b/tests/cmd_help.bats
@@ -81,6 +81,7 @@ teardown() {
   [ "$status" -eq 0 ]
   [[ "$output" == *"git gtr clean"* ]]
   [[ "$output" == *"--merged"* ]]
+  [[ "$output" == *"--to <ref>"* ]]
 }
 
 @test "cmd_help copy shows copy help" {
diff --git a/tests/provider.bats b/tests/provider.bats
index 3491e80..6231ef5 100644
--- a/tests/provider.bats
+++ b/tests/provider.bats
@@ -52,3 +52,134 @@ setup() {
   run extract_hostname ""
   [ "$status" -ne 0 ]
 }
+
+@test "normalize_target_ref strips refs/heads prefix" {
+  result=$(normalize_target_ref "refs/heads/main")
+  [ "$result" = "main" ]
+}
+
+@test "normalize_target_ref strips refs/remotes prefix" {
+  result=$(normalize_target_ref "refs/remotes/origin/release/1.0")
+  [ "$result" = "release/1.0" ]
+}
+
+@test "normalize_target_ref strips remote prefix when remote ref exists" {
+  git remote remove upstream >/dev/null 2>&1 || true
+  run git remote add upstream https://example.com/repo.git
+  [ "$status" -eq 0 ]
+  run git update-ref refs/remotes/upstream/main HEAD
+  [ "$status" -eq 0 ]
+
+  result=$(normalize_target_ref "upstream/main")
+  [ "$result" = "main" ]
+}
+
+# ── check_branch_merged ───────────────────────────────────────────────────────
+
+@test "check_branch_merged passes normalized base ref and limit to gh" {
+  gh() {
+    [ "$1" = "pr" ] || return 1
+    [ "$2" = "list" ] || return 1
+    [ "$3" = "--head" ] || return 1
+    [ "$4" = "feature/test" ] || return 1
+    [ "$5" = "--state" ] || return 1
+    [ "$6" = "merged" ] || return 1
+    [ "$7" = "--limit" ] || return 1
+    [ "$8" = "1000" ] || return 1
+    [ "$9" = "--base" ] || return 1
+    [ "${10}" = "main" ] || return 1
+    [ "${11}" = "--json" ] || return 1
+    [ "${12}" = "state,headRefOid" ] || return 1
+    [ "${13}" = "--jq" ] || return 1
+    [[ "${14}" == *'.headRefOid == "abc123"'* ]] || return 1
+    printf "1"
+  }
+
+  run check_branch_merged github feature/test refs/heads/main abc123
+  [ "$status" -eq 0 ]
+}
+
+@test "check_branch_merged rejects reused GitHub branch names with different HEAD" {
+  gh() {
+    printf "0"
+  }
+
+  run check_branch_merged github feature/test main def456
+  [ "$status" -eq 1 ]
+}
+
+@test "check_branch_merged passes target branch and branch tip to glab" {
+  glab() {
+    [ "$1" = "mr" ] || return 1
+    [ "$2" = "list" ] || return 1
+    [ "$3" = "--source-branch" ] || return 1
+    [ "$4" = "feature/test" ] || return 1
+    [ "$5" = "--merged" ] || return 1
+    [ "$6" = "--all" ] || return 1
+    [ "$7" = "--output" ] || return 1
+    [ "$8" = "json" ] || return 1
+    [ "${9}" = "--target-branch" ] || return 1
+    [ "${10}" = "main" ] || return 1
+    printf '[{"iid":1,"sha":"abc123"}]'
+  }
+
+  run check_branch_merged gitlab feature/test origin/main abc123
+  [ "$status" -eq 0 ]
+}
+
+@test "check_branch_merged rejects reused GitLab branch names with different HEAD" {
+  glab() {
+    [ "$1" = "mr" ] || return 1
+    [ "$2" = "list" ] || return 1
+    [ "$3" = "--source-branch" ] || return 1
+    [ "$4" = "feature/test" ] || return 1
+    [ "$5" = "--merged" ] || return 1
+    [ "$6" = "--all" ] || return 1
+    [ "$7" = "--output" ] || return 1
+    [ "$8" = "json" ] || return 1
+    [ "${9}" = "--target-branch" ] || return 1
+    [ "${10}" = "main" ] || return 1
+    printf '[{"iid":1,"sha":"old123"}]'
+  }
+
+  run check_branch_merged gitlab feature/test main def456
+  [ "$status" -eq 1 ]
+}
+
+@test "check_branch_merged accepts GitLab diff_refs head SHA matches" {
+  glab() {
+    [ "$1" = "mr" ] || return 1
+    [ "$2" = "list" ] || return 1
+    [ "$3" = "--source-branch" ] || return 1
+    [ "$4" = "feature/test" ] || return 1
+    [ "$5" = "--merged" ] || return 1
+    [ "$6" = "--all" ] || return 1
+    [ "$7" = "--output" ] || return 1
+    [ "$8" = "json" ] || return 1
+    [ "${9}" = "--target-branch" ] || return 1
+    [ "${10}" = "main" ] || return 1
+    printf '[{"iid":1,"diff_refs":{"head_sha":"abc123"}}]'
+  }
+
+  run check_branch_merged gitlab feature/test main abc123
+  [ "$status" -eq 0 ]
+}
+
+@test "check_branch_merged still accepts GitLab merged MR without branch tip" {
+  glab() {
+    [ "$1" = "mr" ] || return 1
+    [ "$2" = "list" ] || return 1
+    [ "$3" = "--source-branch" ] || return 1
+    [ "$4" = "feature/test" ] || return 1
+    [ "$5" = "--merged" ] || return 1
+    [ "$6" = "--all" ] || return 1
+    [ "$7" = "--output" ] || return 1
+    [ "$8" = "json" ] || return 1
+    [ "${9}" = "--target-branch" ] || return 1
+    [ "${10}" = "main" ] || return 1
+    printf '[{"iid":1}]'
+  }
+
+  run check_branch_merged gitlab feature/test main
+  [ "$status" -eq 0 ]
+}