diff --git a/.claude/skills/setup-agent-team/discovery.sh b/.claude/skills/setup-agent-team/discovery.sh
index adede4f6..7384705d 100755
--- a/.claude/skills/setup-agent-team/discovery.sh
+++ b/.claude/skills/setup-agent-team/discovery.sh
@@ -517,15 +517,32 @@ run_team_cycle() {
     git fetch --prune origin 2>/dev/null || true
     git pull --rebase origin main 2>/dev/null || true
 
-    # --- Pre-cycle cleanup: stale worktrees ---
-    log_info "Pre-cycle cleanup: stale worktrees..."
+    # --- Pre-cycle cleanup: stale worktrees and branches ---
+    log_info "Pre-cycle cleanup..."
     git worktree prune 2>/dev/null || true
     if [[ -d "${WORKTREE_BASE}" ]]; then
         rm -rf "${WORKTREE_BASE}" 2>/dev/null || true
         log_info "Removed stale ${WORKTREE_BASE} directory"
     fi
 
-    # Note: branch pruning and PR management is handled by the security team
+    # Delete merged discovery-related remote branches
+    # Discovery agents create branches like: add-*, impl-*, gap-filler-*, {cloud}-{agent}
+    MERGED_BRANCHES=$(git branch -r --merged origin/main | grep -v 'origin/main\|origin/HEAD' | grep -E 'origin/(add-|impl-|gap-filler-)' | sed 's|origin/||' | tr -d ' ') || true
+    for branch in $MERGED_BRANCHES; do
+        if [[ -n "$branch" ]]; then
+            git push origin --delete "$branch" 2>&1 && log_info "Deleted merged branch: $branch" || true
+        fi
+    done
+
+    # Delete stale local discovery-related branches
+    LOCAL_BRANCHES=$(git branch --list 'add-*' --list 'impl-*' --list 'gap-filler-*' | tr -d ' *') || true
+    for branch in $LOCAL_BRANCHES; do
+        if [[ -n "$branch" ]]; then
+            git branch -D "$branch" 2>/dev/null || true
+        fi
+    done
+
+    log_info "Pre-cycle cleanup done."
 
     # Set up worktree directory for parallel agent work
     mkdir -p "${WORKTREE_BASE}"
diff --git a/.claude/skills/setup-agent-team/refactor.sh b/.claude/skills/setup-agent-team/refactor.sh
index 75d7324a..758d42df 100755
--- a/.claude/skills/setup-agent-team/refactor.sh
+++ b/.claude/skills/setup-agent-team/refactor.sh
@@ -86,14 +86,30 @@ if [[ "${RUN_MODE}" == "refactor" ]]; then
     # Reset main checkout to origin/main
     git reset --hard origin/main 2>&1 | tee -a "${LOG_FILE}" || true
 
-    log "Pre-cycle cleanup: stale worktrees..."
+    log "Pre-cycle cleanup: stale worktrees and branches..."
     git worktree prune 2>&1 | tee -a "${LOG_FILE}" || true
     if [[ -d "${WORKTREE_BASE}" ]]; then
         rm -rf "${WORKTREE_BASE}" 2>&1 | tee -a "${LOG_FILE}" || true
         log "Removed stale ${WORKTREE_BASE} directory"
     fi
 
-    # Note: branch pruning and PR management is handled by the security team
+    # Delete merged refactor-related remote branches (fix/*, refactor/*, test/*, ux/*)
+    MERGED_BRANCHES=$(git branch -r --merged origin/main | grep -v 'origin/main\|origin/HEAD' | grep -E 'origin/(fix/|refactor/|test/|ux/)' | sed 's|origin/||' | tr -d ' ') || true
+    for branch in $MERGED_BRANCHES; do
+        if [[ -n "$branch" ]]; then
+            git push origin --delete "$branch" 2>&1 | tee -a "${LOG_FILE}" && log "Deleted merged branch: $branch" || true
+        fi
+    done
+
+    # Delete stale local refactor-related branches
+    LOCAL_BRANCHES=$(git branch --list 'fix/*' --list 'refactor/*' --list 'test/*' --list 'ux/*' | tr -d ' *') || true
+    for branch in $LOCAL_BRANCHES; do
+        if [[ -n "$branch" ]]; then
+            git branch -D "$branch" 2>&1 | tee -a "${LOG_FILE}" || true
+        fi
+    done
+
+    log "Pre-cycle cleanup done."
 fi
 
 # Launch Claude Code with mode-specific prompt
diff --git a/.claude/skills/setup-agent-team/security.sh b/.claude/skills/setup-agent-team/security.sh
index 7655b5dc..4675d53f 100644
--- a/.claude/skills/setup-agent-team/security.sh
+++ b/.claude/skills/setup-agent-team/security.sh
@@ -115,10 +115,35 @@ if [[ "${RUN_MODE}" == "team_building" ]] || [[ "${RUN_MODE}" == "triage" ]]; th
     log "Issue: #${ISSUE_NUM}"
 fi
 
-# Fetch latest refs (read-only, safe for concurrent runs)
-log "Fetching latest refs..."
+# Pre-cycle cleanup (stale branches, worktrees from prior runs)
+log "Pre-cycle cleanup..."
 git fetch --prune origin 2>&1 | tee -a "${LOG_FILE}" || true
 
+# Clean stale worktrees
+git worktree prune 2>&1 | tee -a "${LOG_FILE}" || true
+if [[ -d "${WORKTREE_BASE}" ]]; then
+    rm -rf "${WORKTREE_BASE}" 2>&1 | tee -a "${LOG_FILE}" || true
+    log "Removed stale ${WORKTREE_BASE} directory"
+fi
+
+# Delete merged security-related remote branches (team-building/*, review-pr-*)
+MERGED_BRANCHES=$(git branch -r --merged origin/main | grep -E 'origin/(team-building/|review-pr-)' | sed 's|origin/||' | tr -d ' ') || true
+for branch in $MERGED_BRANCHES; do
+    if [[ -n "$branch" ]]; then
+        git push origin --delete "$branch" 2>&1 | tee -a "${LOG_FILE}" && log "Deleted merged branch: $branch" || true
+    fi
+done
+
+# Delete stale local security-related branches
+LOCAL_BRANCHES=$(git branch --list 'team-building/*' --list 'review-pr-*' | tr -d ' *') || true
+for branch in $LOCAL_BRANCHES; do
+    if [[ -n "$branch" ]]; then
+        git branch -D "$branch" 2>&1 | tee -a "${LOG_FILE}" || true
+    fi
+done
+
+log "Pre-cycle cleanup done."
+
 # Launch Claude Code with mode-specific prompt
 log "Launching ${RUN_MODE} cycle..."