diff --git a/bin/gstack-patch-names b/bin/gstack-patch-names
new file mode 100755
index 00000000..bef02aae
--- /dev/null
+++ b/bin/gstack-patch-names
@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+# gstack-patch-names — patch name: field in SKILL.md frontmatter for prefix mode
+# Usage: gstack-patch-names <gstack-dir> <true|false|1|0>
+set -euo pipefail
+
+GSTACK_DIR="$1"
+DO_PREFIX="$2"
+
+# Normalize prefix arg
+case "$DO_PREFIX" in true|1) DO_PREFIX=1 ;; *) DO_PREFIX=0 ;; esac
+
+PATCHED=0
+for skill_dir in "$GSTACK_DIR"/*/; do
+  [ -f "$skill_dir/SKILL.md" ] || continue
+  dir_name="$(basename "$skill_dir")"
+  [ "$dir_name" = "node_modules" ] && continue
+  cur=$(grep -m1 '^name:' "$skill_dir/SKILL.md" 2>/dev/null | sed 's/^name:[[:space:]]*//' | tr -d '[:space:]' || true)
+  [ -z "$cur" ] && continue
+  [ "$cur" = "gstack" ] && continue  # never prefix root skill
+  if [ "$DO_PREFIX" -eq 1 ]; then
+    case "$cur" in gstack-*) continue ;; esac
+    new="gstack-$cur"
+  else
+    case "$cur" in gstack-*) ;; *) continue ;; esac
+    [ "$dir_name" = "$cur" ] && continue  # inherently prefixed (gstack-upgrade)
+    new="${cur#gstack-}"
+  fi
+  tmp="$(mktemp "${skill_dir}/SKILL.md.XXXXXX")"
+  sed "1,/^---$/s/^name:[[:space:]]*${cur}/name: ${new}/" "$skill_dir/SKILL.md" > "$tmp" && mv "$tmp" "$skill_dir/SKILL.md"
+  PATCHED=$((PATCHED + 1))
+done
+if [ "$PATCHED" -gt 0 ]; then
+  echo "  patched name: field in $PATCHED skills"
+fi
diff --git a/bin/gstack-relink b/bin/gstack-relink
index 49d0ccac..4647f6df 100755
--- a/bin/gstack-relink
+++ b/bin/gstack-relink
@@ -66,6 +66,9 @@ for skill_dir in "$INSTALL_DIR"/*/; do
   SKILL_COUNT=$((SKILL_COUNT + 1))
 done
 
+# Patch SKILL.md name: fields to match prefix setting
+"$INSTALL_DIR/bin/gstack-patch-names" "$INSTALL_DIR" "$PREFIX"
+
 if [ "$PREFIX" = "true" ]; then
   echo "Relinked $SKILL_COUNT skills as gstack-*"
 else
diff --git a/scripts/gen-skill-docs.ts b/scripts/gen-skill-docs.ts
index 94f39101..ec495189 100644
--- a/scripts/gen-skill-docs.ts
+++ b/scripts/gen-skill-docs.ts
@@ -472,3 +472,16 @@ if (failures.length > 0 && HOST_ARG_VAL === 'all') {
   if (failures.some(f => f.host === 'claude')) process.exit(1);
 }
 // Single host dry-run failure already handled above
+
+// After all hosts processed, warn if prefix patches may need re-applying
+if (!DRY_RUN) {
+  try {
+    const configPath = path.join(process.env.HOME || '', '.gstack', 'config.yaml');
+    if (fs.existsSync(configPath)) {
+      const config = fs.readFileSync(configPath, 'utf-8');
+      if (/^skill_prefix:\s*true/m.test(config)) {
+        console.log('\nNote: skill_prefix is true. Run gstack-relink to re-apply name: patches.');
+      }
+    }
+  } catch { /* non-fatal */ }
+}
diff --git a/setup b/setup
index d2836245..609311d5 100755
--- a/setup
+++ b/setup
@@ -567,6 +567,7 @@ if [ "$INSTALL_CLAUDE" -eq 1 ]; then
       cleanup_prefixed_claude_symlinks "$SOURCE_GSTACK_DIR" "$INSTALL_SKILLS_DIR"
     fi
     link_claude_skill_dirs "$SOURCE_GSTACK_DIR" "$INSTALL_SKILLS_DIR"
+    "$SOURCE_GSTACK_DIR/bin/gstack-patch-names" "$SOURCE_GSTACK_DIR" "$SKILL_PREFIX"
     if [ "$LOCAL_INSTALL" -eq 1 ]; then
       echo "gstack ready (project-local)."
       echo "  skills: $INSTALL_SKILLS_DIR"