diff --git a/README.md b/README.md
index 7fb6948..9228790 100644
--- a/README.md
+++ b/README.md
@@ -243,9 +243,9 @@ cn alerts reset                    # Back to default (idle_prompt only)
 | `TaskCreated`        | Claude agent-team task was created             |
 | `TaskCompleted`      | Claude agent-team task completed               |
 
-Alert-type matching applies to Claude Code notification hooks and Gemini CLI notification hooks. `ask_user` is a Claude-only `PreToolUse` hook for `AskUserQuestion`; it is applied immediately when Claude notifications are already enabled. Claude Code agent/team events are separate hook events and are opt-in via `cn alerts add SubagentStop`, `cn alerts add TeammateIdle`, or `cn alerts add TaskCompleted`.
+Alert-type matching applies to Claude Code notification hooks and Gemini CLI notification hooks. Changes are applied immediately when Claude notifications are already enabled; otherwise, run `cn on` after choosing the alert types. `ask_user` is a Claude-only `PreToolUse` hook for `AskUserQuestion`. Claude Code agent/team events are separate hook events and are opt-in via `cn alerts add SubagentStop`, `cn alerts add TeammateIdle`, or `cn alerts add TaskCompleted`.
 
-Agent-team and subagent workflows can be noisy if `permission_prompt` is enabled. If you only want idle pings, run `cn alerts remove permission_prompt && cn on`. Codex currently uses completion events from `notify`, so `permission_prompt` and `idle_prompt` settings do not change Codex behavior.
+Agent-team and subagent workflows can be noisy if `permission_prompt` is enabled. If you only want idle pings, run `cn alerts remove permission_prompt`. Codex currently uses completion events from `notify`, so `permission_prompt` and `idle_prompt` settings do not change Codex behavior.
 
 ### Slack And Discord
 
diff --git a/lib/code-notify/commands/global.sh b/lib/code-notify/commands/global.sh
index 0779e6c..8311bec 100755
--- a/lib/code-notify/commands/global.sh
+++ b/lib/code-notify/commands/global.sh
@@ -1129,6 +1129,17 @@ show_available_alert_types() {
     echo "Aliases like ${CYAN}subagent_stop${RESET}, ${CYAN}teammate-idle${RESET}, and ${CYAN}task_completed${RESET} are accepted."
 }
 
+# Rewrite enabled Claude hooks after an alert-type change. The previous matcher
+# no longer passes is_enabled_globally(), so detect the stable managed Stop hook
+# instead.
+apply_alert_types_to_enabled_hooks() {
+    if ! has_managed_global_claude_hooks; then
+        return 2
+    fi
+
+    enable_hooks_in_settings
+}
+
 # Add an alert type
 add_alert_type() {
     local type
@@ -1141,20 +1152,31 @@ add_alert_type() {
         return 1
     fi
 
+    local already_enabled=0
     if is_notify_type_enabled "$type"; then
-        warning "$type is already enabled"
-        return 0
+        already_enabled=1
+    else
+        add_notify_type "$type"
     fi
 
-    add_notify_type "$type"
+    local applied=0 apply_result=0
+    apply_alert_types_to_enabled_hooks || apply_result=$?
+    if [[ $apply_result -eq 0 ]]; then
+        applied=1
+    elif [[ $apply_result -ne 2 ]]; then
+        error "Failed to apply alert types to enabled Claude hooks"
+        return 1
+    fi
 
-    # For ask_user: register PreToolUse hook immediately
-    if [[ "$type" == "ask_user" ]] && is_tool_enabled "claude"; then
-        register_ask_user_hook "$GLOBAL_SETTINGS_FILE" "$(get_global_claude_pre_tool_use_command)"
+    if [[ $already_enabled -eq 1 ]]; then
+        warning "$type is already enabled"
+    else
+        success "Added: $type"
     fi
 
-    success "Added: $type"
-    if [[ "$type" != "ask_user" ]]; then
+    if [[ $applied -eq 1 ]]; then
+        info "Applied to enabled Claude hooks"
+    elif [[ "$type" != "ask_user" ]]; then
         echo ""
         info "Run ${CYAN}cn on${RESET} to apply changes"
     fi
@@ -1172,20 +1194,30 @@ remove_alert_type() {
         return 1
     fi
 
-    if ! is_notify_type_enabled "$type"; then
-        warning "$type is not currently enabled"
-        return 0
+    local was_enabled=0
+    if is_notify_type_enabled "$type"; then
+        was_enabled=1
+        remove_notify_type "$type"
     fi
 
-    remove_notify_type "$type"
+    local applied=0 apply_result=0
+    apply_alert_types_to_enabled_hooks || apply_result=$?
+    if [[ $apply_result -eq 0 ]]; then
+        applied=1
+    elif [[ $apply_result -ne 2 ]]; then
+        error "Failed to apply alert types to enabled Claude hooks"
+        return 1
+    fi
 
-    # For ask_user: unregister PreToolUse hook immediately
-    if [[ "$type" == "ask_user" ]] && is_tool_enabled "claude"; then
-        unregister_ask_user_hook "$GLOBAL_SETTINGS_FILE" "$(get_global_claude_pre_tool_use_command)"
+    if [[ $was_enabled -eq 0 ]]; then
+        warning "$type is not currently enabled"
+    else
+        success "Removed: $type"
     fi
 
-    success "Removed: $type"
-    if [[ "$type" != "ask_user" ]]; then
+    if [[ $applied -eq 1 ]]; then
+        info "Applied to enabled Claude hooks"
+    elif [[ "$type" != "ask_user" ]]; then
         echo ""
         info "Run ${CYAN}cn on${RESET} to apply changes"
     fi
@@ -1195,8 +1227,17 @@ remove_alert_type() {
 reset_alert_types() {
     reset_notify_types
     success "Reset to default: idle_prompt"
-    echo ""
-    info "Run ${CYAN}cn on${RESET} to apply changes"
+    local apply_result=0
+    apply_alert_types_to_enabled_hooks || apply_result=$?
+    if [[ $apply_result -eq 0 ]]; then
+        info "Applied to enabled Claude hooks"
+    elif [[ $apply_result -ne 2 ]]; then
+        error "Failed to apply alert types to enabled Claude hooks"
+        return 1
+    else
+        echo ""
+        info "Run ${CYAN}cn on${RESET} to apply changes"
+    fi
 }
 
 # Show alerts help
diff --git a/lib/code-notify/core/config.sh b/lib/code-notify/core/config.sh
index f953c09..7b1cf1e 100755
--- a/lib/code-notify/core/config.sh
+++ b/lib/code-notify/core/config.sh
@@ -519,6 +519,46 @@ is_enabled_globally() {
     [[ -f "$GLOBAL_HOOKS_FILE" ]]
 }
 
+# Check for an installed Code-Notify Claude hook without requiring its
+# Notification matcher to match the current alert-type configuration. This is
+# used when alert types change, because the matcher is stale until it is
+# rewritten.
+has_managed_global_claude_hooks() {
+    local file="${1:-$GLOBAL_SETTINGS_FILE}"
+    local stop_cmd
+    stop_cmd="$(get_global_claude_stop_command)"
+
+    if [[ -f "$file" ]]; then
+        if has_jq; then
+            jq -e --arg cmd "$stop_cmd" '
+                any(.hooks.Stop[]?.hooks[]?;
+                    (.type // "") == "command" and (.command // "") == $cmd
+                )
+            ' "$file" >/dev/null 2>&1 && return 0
+        elif has_python3; then
+            python3 - "$file" "$stop_cmd" <<'PYTHON' >/dev/null 2>&1 && return 0
+import json
+import sys
+
+file_path, stop_cmd = sys.argv[1:3]
+with open(file_path, "r") as fh:
+    settings = json.load(fh)
+
+for entry in settings.get("hooks", {}).get("Stop", []):
+    for hook in entry.get("hooks", []):
+        if hook.get("type") == "command" and hook.get("command") == stop_cmd:
+            raise SystemExit(0)
+
+raise SystemExit(1)
+PYTHON
+        else
+            grep -qF "\"command\": \"$stop_cmd\"" "$file" && return 0
+        fi
+    fi
+
+    [[ -f "$GLOBAL_HOOKS_FILE" ]]
+}
+
 # Check if notifications are enabled for current project
 is_enabled_project() {
     local project_root=$(get_project_root 2>/dev/null || echo "$PWD")
diff --git a/scripts/run_tests.sh b/scripts/run_tests.sh
index bf472b9..9669cd3 100755
--- a/scripts/run_tests.sh
+++ b/scripts/run_tests.sh
@@ -251,6 +251,13 @@ else
     test_fail "ask_user alert preservation failed"
 fi
 
+test_start "alert changes auto-apply"
+if bash tests/test-alert-auto-apply.sh >/dev/null 2>&1; then
+    test_pass
+else
+    test_fail "alert changes were not applied to enabled Claude hooks"
+fi
+
 # Test 24: omp (Oh My Pi) extension install/detect/notify
 test_start "omp extension support"
 if bash tests/test-omp-extension.sh >/dev/null 2>&1; then
diff --git a/tests/test-alert-auto-apply.sh b/tests/test-alert-auto-apply.sh
new file mode 100755
index 0000000..babb8e0
--- /dev/null
+++ b/tests/test-alert-auto-apply.sh
@@ -0,0 +1,80 @@
+#!/bin/bash
+
+set -euo pipefail
+
+ROOT_DIR="$(cd "$(dirname "$0")/.." && pwd)"
+test_dir="$(mktemp -d)"
+trap 'rm -rf "$test_dir"' EXIT
+
+export HOME="$test_dir/home"
+export CLAUDE_HOME="$HOME/.claude"
+export CLAUDE_SETTINGS_HOME="$CLAUDE_HOME"
+mkdir -p "$CLAUDE_HOME/notifications"
+
+source "$ROOT_DIR/lib/code-notify/utils/colors.sh"
+source "$ROOT_DIR/lib/code-notify/core/config.sh"
+source "$ROOT_DIR/lib/code-notify/commands/global.sh"
+
+notify_script="$test_dir/notify.sh"
+get_notify_script() {
+    printf '%s\n' "$notify_script"
+}
+
+fail() {
+    echo "FAIL: $1" >&2
+    exit 1
+}
+
+get_claude_matcher() {
+    python3 - "$GLOBAL_SETTINGS_FILE" "$notify_script" <<'PYTHON'
+import json
+import sys
+
+settings_file, notify_script = sys.argv[1:3]
+with open(settings_file, "r") as fh:
+    settings = json.load(fh)
+
+command = f"{notify_script} notification claude"
+for entry in settings.get("hooks", {}).get("Notification", []):
+    if any(hook.get("command") == command for hook in entry.get("hooks", [])):
+        print(entry.get("matcher", ""), end="")
+        break
+PYTHON
+}
+
+enable_hooks_in_settings
+[[ "$(get_claude_matcher)" == "idle_prompt" ]] || fail "initial matcher is incorrect"
+
+add_alert_type permission_prompt >/dev/null
+[[ "$(get_claude_matcher)" == "idle_prompt|permission_prompt" ]] ||
+    fail "adding permission_prompt did not immediately refresh Claude hooks"
+
+# Repeating the command must also repair a stale matcher left by an older
+# version that changed notify-types without rewriting settings.json.
+python3 - "$GLOBAL_SETTINGS_FILE" <<'PYTHON'
+import json
+import sys
+
+path = sys.argv[1]
+with open(path, "r") as fh:
+    settings = json.load(fh)
+settings["hooks"]["Notification"][0]["matcher"] = "idle_prompt"
+with open(path, "w") as fh:
+    json.dump(settings, fh, indent=2)
+    fh.write("\n")
+PYTHON
+
+add_alert_type permission_prompt >/dev/null
+[[ "$(get_claude_matcher)" == "idle_prompt|permission_prompt" ]] ||
+    fail "re-adding an enabled type did not repair the stale matcher"
+
+remove_alert_type permission_prompt >/dev/null
+[[ "$(get_claude_matcher)" == "idle_prompt" ]] ||
+    fail "removing permission_prompt did not immediately refresh Claude hooks"
+
+add_alert_type permission_prompt >/dev/null
+reset_alert_types >/dev/null
+[[ "$(get_claude_matcher)" == "idle_prompt" ]] ||
+    fail "reset did not immediately refresh Claude hooks"
+
+echo "PASS: alert changes automatically refresh enabled Claude hooks"