diff --git a/CHANGELOG.md b/CHANGELOG.md
index 893769a..0cf2d43 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [Unreleased]
+
+- fix: handle `gh pr merge` in worktree context - detect worktree and use remote-only merge strategy to avoid `fatal: 'main' is already used by worktree` error (#3)
+
 ## [1.0.0] - 2026-02-21
 
 Initial release. Extracted from [agentsys](https://github.com/agent-sh/agentsys) monorepo.
diff --git a/commands/ship-deployment.md b/commands/ship-deployment.md
index 2de54c4..51357ca 100644
--- a/commands/ship-deployment.md
+++ b/commands/ship-deployment.md
@@ -184,6 +184,14 @@ Proceeding to production...
 ### Merge to Production Branch
 
 ```bash
+# Worktree check must come first - multi-branch deployment requires branch checkout
+if [ -f "$(git rev-parse --show-toplevel 2>/dev/null)/.git" ]; then
+  MAIN_REPO=$(dirname "$(git rev-parse --git-common-dir 2>/dev/null)")
+  echo "[ERROR] Multi-branch deployment is not supported from a worktree"
+  echo "Run from the main repo: cd $MAIN_REPO"
+  exit 1
+fi
+
 echo "Merging $MAIN_BRANCH → $PROD_BRANCH..."
 
 git checkout $PROD_BRANCH
@@ -283,9 +291,18 @@ fi
 
 ```bash
 rollback_production() {
+  # Worktree check must come first
+  if [ -f "$(git rev-parse --show-toplevel 2>/dev/null)/.git" ]; then
+    MAIN_REPO=$(dirname "$(git rev-parse --git-common-dir 2>/dev/null)")
+    echo "[ERROR] Rollback is not supported from a worktree"
+    echo "Run from the main repo: cd $MAIN_REPO"
+    exit 1
+  fi
+
   echo "========================================"
   echo "ROLLBACK INITIATED"
   echo "========================================"
+
   echo "WARNING: Force pushing to $PROD_BRANCH to revert"
 
   git checkout $PROD_BRANCH
diff --git a/commands/ship-error-handling.md b/commands/ship-error-handling.md
index dc7cbe4..534cc2d 100644
--- a/commands/ship-error-handling.md
+++ b/commands/ship-error-handling.md
@@ -227,12 +227,22 @@ git push
 ### Cancel and Cleanup
 
 ```bash
-# If you need to abandon the PR
-gh pr close $PR_NUMBER --delete-branch
+# Detect worktree
+IS_WORKTREE="false"
+if [ -f "$(git rev-parse --show-toplevel 2>/dev/null)/.git" ]; then
+  IS_WORKTREE="true"
+fi
 
-# Clean up local
-git checkout $MAIN_BRANCH
-git branch -D $CURRENT_BRANCH
+if [ "$IS_WORKTREE" = "true" ]; then
+  # In worktree: close PR and delete remote branch separately
+  gh pr close $PR_NUMBER
+  git push origin --delete "$CURRENT_BRANCH" 2>&1 || echo "[WARN] Remote branch deletion failed - may need manual cleanup"
+  echo "[OK] PR closed (worktree mode - local cleanup deferred to worktree removal)"
+else
+  gh pr close $PR_NUMBER --delete-branch
+  git checkout $MAIN_BRANCH
+  git branch -D $CURRENT_BRANCH
+fi
 ```
 
 ## Exit Codes
diff --git a/commands/ship.md b/commands/ship.md
index c03a768..a4ecb50 100644
--- a/commands/ship.md
+++ b/commands/ship.md
@@ -348,17 +348,37 @@ fi
 
 echo "[OK] All comments resolved"
 
-# 3. Merge with strategy (default: squash)
+# 3. Detect if running from a worktree
+IS_WORKTREE="false"
+if [ -f "$(git rev-parse --show-toplevel 2>/dev/null)/.git" ]; then
+  IS_WORKTREE="true"
+  echo "[INFO] Running from worktree - using remote-only merge strategy"
+fi
+
+# 4. Merge with strategy (default: squash)
 STRATEGY=${STRATEGY:-squash}
-gh pr merge $PR_NUMBER --$STRATEGY --delete-branch
+if [ -z "$OWNER" ] || [ -z "$REPO" ]; then
+  echo "[ERROR] Failed to extract repo owner/name"
+  exit 1
+fi
 
-# Update local
-git checkout $MAIN_BRANCH
-git pull origin $MAIN_BRANCH
+if [ "$IS_WORKTREE" = "true" ]; then
+  # In worktree: merge without --delete-branch (it tries to checkout main locally)
+  gh pr merge $PR_NUMBER --$STRATEGY --repo "$OWNER/$REPO"
+  # Delete remote branch separately
+  git push origin --delete "$CURRENT_BRANCH" 2>&1 || echo "[WARN] Remote branch deletion failed - may need manual cleanup"
+  # Get merge SHA from the PR metadata (avoids race condition with fetch)
+  MERGE_SHA=$(gh pr view $PR_NUMBER --repo "$OWNER/$REPO" --json mergeCommit --jq '.mergeCommit.oid')
+else
+  gh pr merge $PR_NUMBER --$STRATEGY --delete-branch
+  # Update local
+  git checkout $MAIN_BRANCH
+  git pull origin $MAIN_BRANCH
+  MERGE_SHA=$(git rev-parse HEAD)
+fi
 
 # Update repo-map if it exists (non-blocking)
 node -e "const { getPluginRoot } = require('@agentsys/lib/cross-platform'); const pluginRoot = getPluginRoot('ship'); if (!pluginRoot) { console.log('Plugin root not found, skipping repo-map'); process.exit(0); } const repoMap = require(\`\${pluginRoot}/lib/repo-map\`); if (repoMap.exists(process.cwd())) { repoMap.update(process.cwd(), {}).then(() => console.log('[OK] Repo-map updated')).catch((e) => console.log('[WARN] Repo-map update failed: ' + e.message)); } else { console.log('Repo-map not found, skipping'); }" || true
-MERGE_SHA=$(git rev-parse HEAD)
 echo "[OK] Merged PR #$PR_NUMBER at $MERGE_SHA"
 ```
 </phase-6>
@@ -438,9 +458,20 @@ if (workflowState) {
 ### Local Branch Cleanup
 
 ```bash
-git checkout $MAIN_BRANCH
-# Feature branch already deleted by --delete-branch
-git branch -D $CURRENT_BRANCH 2>/dev/null || true
+# Re-detect worktree in case Phase 6 was skipped or run separately
+if [ -z "$IS_WORKTREE" ]; then
+  IS_WORKTREE="false"
+  if [ -f "$(git rev-parse --show-toplevel 2>/dev/null)/.git" ]; then
+    IS_WORKTREE="true"
+  fi
+fi
+
+if [ "$IS_WORKTREE" = "true" ]; then
+  echo "[OK] Local branch cleanup deferred (worktree mode - cleaned when worktree is removed)"
+else
+  git checkout $MAIN_BRANCH
+  git branch -D $CURRENT_BRANCH 2>/dev/null || true
+fi
 ```
 
 ## Phase 12: Completion Report