diff --git a/README.md b/README.md
index 27d8c9b..62ba666 100644
--- a/README.md
+++ b/README.md
@@ -61,6 +61,13 @@ Run manually:
 ~/.mosaic/bin/mosaic-link-runtime-assets
 ```
 
+Prune migrated legacy backups from runtime folders (dry-run by default):
+
+```bash
+~/.mosaic/bin/mosaic-prune-legacy-runtime --runtime claude
+~/.mosaic/bin/mosaic-prune-legacy-runtime --runtime claude --apply
+```
+
 Opt-out during install:
 
 ```bash
diff --git a/bin/mosaic-prune-legacy-runtime b/bin/mosaic-prune-legacy-runtime
new file mode 100755
index 0000000..641804f
--- /dev/null
+++ b/bin/mosaic-prune-legacy-runtime
@@ -0,0 +1,95 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.mosaic}"
+RUNTIME="claude"
+APPLY=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Remove legacy runtime files that were preserved as *.mosaic-bak-* after Mosaic linking.
+Only removes backups when the active file is a symlink to ~/.mosaic.
+
+Options:
+  --runtime <name>   Runtime to prune (default: claude)
+  --apply            Perform deletions (default: dry-run)
+  -h, --help         Show help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --runtime)
+      [[ $# -lt 2 ]] && { echo "Missing value for --runtime" >&2; exit 1; }
+      RUNTIME="$2"
+      shift 2
+      ;;
+    --apply)
+      APPLY=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+case "$RUNTIME" in
+  claude)
+    TARGET_ROOT="$HOME/.claude"
+    ;;
+  *)
+    echo "Unsupported runtime: $RUNTIME" >&2
+    exit 1
+    ;;
+esac
+
+if [[ ! -d "$TARGET_ROOT" ]]; then
+  echo "[mosaic-prune] Runtime directory not found: $TARGET_ROOT" >&2
+  exit 1
+fi
+
+mosaic_real="$(readlink -f "$MOSAIC_HOME")"
+count_candidates=0
+count_deletable=0
+
+while IFS= read -r -d '' bak; do
+  count_candidates=$((count_candidates + 1))
+
+  base="${bak%%.mosaic-bak-*}"
+  if [[ ! -L "$base" ]]; then
+    continue
+  fi
+
+  base_real="$(readlink -f "$base" 2>/dev/null || true)"
+  if [[ -z "$base_real" ]]; then
+    continue
+  fi
+
+  if [[ "$base_real" != "$mosaic_real"/* ]]; then
+    continue
+  fi
+
+  count_deletable=$((count_deletable + 1))
+  if [[ $APPLY -eq 1 ]]; then
+    rm -f "$bak"
+    echo "[mosaic-prune] deleted: $bak"
+  else
+    echo "[mosaic-prune] would delete: $bak"
+  fi
+done < <(find "$TARGET_ROOT" -type f -name '*.mosaic-bak-*' -print0)
+
+if [[ $APPLY -eq 1 ]]; then
+  echo "[mosaic-prune] complete: deleted=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+else
+  echo "[mosaic-prune] dry-run: deletable=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+  echo "[mosaic-prune] re-run with --apply to delete"
+fi