diff --git a/v3/@claude-flow/cli/.claude/hooks/hook-bridge.sh b/v3/@claude-flow/cli/.claude/hooks/hook-bridge.sh
new file mode 100755
index 0000000000..261b405317
--- /dev/null
+++ b/v3/@claude-flow/cli/.claude/hooks/hook-bridge.sh
@@ -0,0 +1,100 @@
+#!/bin/bash
+# hook-bridge.sh - Bridges Claude Code hooks (stdin JSON) to claude-flow CLI
+#
+# Claude Code passes hook context as JSON via stdin, NOT as shell environment
+# variables. This script reads the stdin JSON, extracts the relevant fields
+# using jq, and forwards them as proper CLI arguments.
+#
+# Usage: hook-bridge.sh <mode>
+#
+# Requires: jq (https://jqlang.github.io/jq/)
+
+MODE="${1:-}"
+
+# Read JSON from stdin (Claude Code always pipes hook data this way)
+INPUT=$(cat 2>/dev/null) || INPUT='{}'
+[ -z "$INPUT" ] && INPUT='{}'
+
+# Safe JSON field extraction - returns empty string on missing/null fields
+jf() {
+  echo "$INPUT" | jq -r "$1" 2>/dev/null | grep -v '^null$' || echo ""
+}
+
+case "$MODE" in
+  # -- PreToolUse hooks -----------------------------------------------
+  pre-edit)
+    FILE=$(jf '.tool_input.file_path')
+    [ -z "$FILE" ] && exit 0
+    exec npx @claude-flow/cli@latest hooks pre-edit --file "$FILE"
+    ;;
+
+  pre-command)
+    CMD=$(jf '.tool_input.command')
+    [ -z "$CMD" ] && exit 0
+    exec npx @claude-flow/cli@latest hooks pre-command --command "$CMD"
+    ;;
+
+  pre-task)
+    DESC=$(jf '.tool_input.prompt // .tool_input.description')
+    [ -z "$DESC" ] && exit 0
+    exec npx @claude-flow/cli@latest hooks pre-task --description "$DESC"
+    ;;
+
+  # -- PostToolUse hooks ----------------------------------------------
+  post-edit)
+    FILE=$(jf '.tool_input.file_path')
+    [ -z "$FILE" ] && exit 0
+    exec npx @claude-flow/cli@latest hooks post-edit --file "$FILE" --success true
+    ;;
+
+  post-command)
+    CMD=$(jf '.tool_input.command')
+    [ -z "$CMD" ] && exit 0
+    exec npx @claude-flow/cli@latest hooks post-command --command "$CMD" --success true
+    ;;
+
+  post-task)
+    AGENT_ID=$(jf '.tool_input.description // .tool_input.prompt')
+    [ -z "$AGENT_ID" ] && AGENT_ID="unknown"
+    exec npx @claude-flow/cli@latest hooks post-task --task-id "$AGENT_ID" --success true
+    ;;
+
+  # -- UserPromptSubmit -----------------------------------------------
+  route)
+    PROMPT=$(jf '.prompt')
+    [ -z "$PROMPT" ] && exit 0
+    exec npx @claude-flow/cli@latest hooks route --task "$PROMPT"
+    ;;
+
+  # -- SessionStart ---------------------------------------------------
+  daemon-start)
+    exec npx @claude-flow/cli@latest daemon start --quiet
+    ;;
+
+  session-restore)
+    SID=$(jf '.session_id')
+    if [ -n "$SID" ]; then
+      exec npx @claude-flow/cli@latest hooks session-restore --session-id "$SID"
+    else
+      exec npx @claude-flow/cli@latest hooks session-restore --latest
+    fi
+    ;;
+
+  # -- Stop -----------------------------------------------------------
+  stop-check)
+    echo '{"ok":true}'
+    exit 0
+    ;;
+
+  # -- Notification ---------------------------------------------------
+  notify)
+    MSG=$(jf '.message // .notification_message // .content')
+    [ -z "$MSG" ] && exit 0
+    exec npx @claude-flow/cli@latest memory store --namespace notifications --key "notify" --value "$MSG"
+    ;;
+
+  *)
+    echo "Unknown hook mode: $MODE" >&2
+    exit 1
+    ;;
+esac
diff --git a/v3/@claude-flow/cli/.claude/settings.json b/v3/@claude-flow/cli/.claude/settings.json
index bfbfada31f..8c6127f00c 100644
--- a/v3/@claude-flow/cli/.claude/settings.json
+++ b/v3/@claude-flow/cli/.claude/settings.json
@@ -6,8 +6,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$TOOL_INPUT_file_path\" ] && npx @claude-flow/cli@latest hooks pre-edit --file \"$TOOL_INPUT_file_path\" 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh pre-edit",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -17,8 +17,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$TOOL_INPUT_command\" ] && npx @claude-flow/cli@latest hooks pre-command --command \"$TOOL_INPUT_command\" 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh pre-command",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -28,8 +28,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$TOOL_INPUT_prompt\" ] && npx @claude-flow/cli@latest hooks pre-task --task-id \"task-$(date +%s)\" --description \"$TOOL_INPUT_prompt\" 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh pre-task",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -41,8 +41,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$TOOL_INPUT_file_path\" ] && npx @claude-flow/cli@latest hooks post-edit --file \"$TOOL_INPUT_file_path\" --success \"${TOOL_SUCCESS:-true}\" 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh post-edit",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -52,8 +52,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$TOOL_INPUT_command\" ] && npx @claude-flow/cli@latest hooks post-command --command \"$TOOL_INPUT_command\" --success \"${TOOL_SUCCESS:-true}\" 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh post-command",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -63,8 +63,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$TOOL_RESULT_agent_id\" ] && npx @claude-flow/cli@latest hooks post-task --task-id \"$TOOL_RESULT_agent_id\" --success \"${TOOL_SUCCESS:-true}\" 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh post-task",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -75,8 +75,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$PROMPT\" ] && npx @claude-flow/cli@latest hooks route --task \"$PROMPT\" || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh route",
+            "timeout": 10000,
             "continueOnError": true
           }
         ]
@@ -87,14 +87,14 @@
         "hooks": [
           {
             "type": "command",
-            "command": "npx @claude-flow/cli@latest daemon start --quiet 2>/dev/null || true",
-            "timeout": 5000,
+            "command": ".claude/hooks/hook-bridge.sh daemon-start",
+            "timeout": 10000,
             "continueOnError": true
           },
           {
             "type": "command",
-            "command": "[ -n \"$SESSION_ID\" ] && npx @claude-flow/cli@latest hooks session-restore --session-id \"$SESSION_ID\" 2>/dev/null || true",
-            "timeout": 10000,
+            "command": ".claude/hooks/hook-bridge.sh session-restore",
+            "timeout": 15000,
             "continueOnError": true
           }
         ]
@@ -105,7 +105,7 @@
         "hooks": [
           {
             "type": "command",
-            "command": "echo '{\"ok\": true}'",
+            "command": ".claude/hooks/hook-bridge.sh stop-check",
             "timeout": 1000
           }
         ]
@@ -116,8 +116,8 @@
         "hooks": [
           {
             "type": "command",
-            "command": "[ -n \"$NOTIFICATION_MESSAGE\" ] && npx @claude-flow/cli@latest memory store --namespace notifications --key \"notify-$(date +%s)\" --value \"$NOTIFICATION_MESSAGE\" 2>/dev/null || true",
-            "timeout": 3000,
+            "command": ".claude/hooks/hook-bridge.sh notify",
+            "timeout": 5000,
             "continueOnError": true
           }
         ]
@@ -234,4 +234,4 @@
       "threatModel": true
     }
   }
-}
\ No newline at end of file
+}
diff --git a/v3/@claude-flow/cli/src/init/executor.ts b/v3/@claude-flow/cli/src/init/executor.ts
index 5cde164f74..33d2c3ffdb 100644
--- a/v3/@claude-flow/cli/src/init/executor.ts
+++ b/v3/@claude-flow/cli/src/init/executor.ts
@@ -129,6 +129,7 @@ const DIRECTORIES = {
     '.claude/commands',
     '.claude/agents',
     '.claude/helpers',
+    '.claude/hooks',
   ],
   runtime: [
     '.claude-flow',
@@ -757,6 +758,57 @@ function findSourceHelpersDir(sourceBaseDir?: string): string | null {
   return null;
 }
 
+/**
+ * Write hook-bridge.sh to .claude/hooks/
+ *
+ * This script is required for Claude Code hooks to function correctly.
+ * Claude Code passes hook context as JSON via stdin (not as env vars),
+ * so a bridge script is needed to parse the JSON and forward fields
+ * as proper CLI arguments.
+ */
+async function writeHookBridge(
+  targetDir: string,
+  options: InitOptions,
+  result: InitResult
+): Promise<void> {
+  const hooksDir = path.join(targetDir, '.claude', 'hooks');
+
+  if (!fs.existsSync(hooksDir)) {
+    fs.mkdirSync(hooksDir, { recursive: true });
+  }
+
+  const bridgePath = path.join(hooksDir, 'hook-bridge.sh');
+
+  if (fs.existsSync(bridgePath) && !options.force) {
+    result.skipped.push('.claude/hooks/hook-bridge.sh');
+    return;
+  }
+
+  // Try to copy from package source first
+  const sourceHooksDir = findSourceDir('hooks', options.sourceBaseDir);
+  if (sourceHooksDir) {
+    const sourceBridge = path.join(sourceHooksDir, 'hook-bridge.sh');
+    if (fs.existsSync(sourceBridge)) {
+      fs.copyFileSync(sourceBridge, bridgePath);
+      fs.chmodSync(bridgePath, '755');
+      result.created.files.push('.claude/hooks/hook-bridge.sh');
+      return;
+    }
+  }
+
+  // Fallback: check package's own .claude/hooks directory
+  const packageRoot = path.resolve(__dirname, '..', '..', '..');
+  const packageBridge = path.join(packageRoot, '.claude', 'hooks', 'hook-bridge.sh');
+  if (fs.existsSync(packageBridge)) {
+    fs.copyFileSync(packageBridge, bridgePath);
+    fs.chmodSync(bridgePath, '755');
+    result.created.files.push('.claude/hooks/hook-bridge.sh');
+    return;
+  }
+
+  result.errors.push('Could not find hook-bridge.sh source. Hooks may not function correctly.');
+}
+
 /**
  * Write helper scripts
  */
@@ -767,6 +819,11 @@ async function writeHelpers(
 ): Promise<void> {
   const helpersDir = path.join(targetDir, '.claude', 'helpers');
 
+  // Write hook-bridge.sh (required for Claude Code hooks to work)
+  // Claude Code passes hook context as JSON via stdin, not as env vars.
+  // hook-bridge.sh reads the JSON and forwards fields as CLI arguments.
+  await writeHookBridge(targetDir, options, result);
+
   // Find source helpers directory (works for npm package and local dev)
   const sourceHelpersDir = findSourceHelpersDir(options.sourceBaseDir);
 
diff --git a/v3/@claude-flow/cli/src/init/settings-generator.ts b/v3/@claude-flow/cli/src/init/settings-generator.ts
index c355d9254f..50110ba311 100644
--- a/v3/@claude-flow/cli/src/init/settings-generator.ts
+++ b/v3/@claude-flow/cli/src/init/settings-generator.ts
@@ -143,11 +143,17 @@ function generateStatusLineConfig(options: InitOptions): object {
 
 /**
  * Generate hooks configuration
+ *
+ * IMPORTANT: Claude Code passes hook context as JSON via stdin, NOT as shell
+ * environment variables. The hook-bridge.sh script reads stdin JSON with jq
+ * and forwards the extracted fields as proper CLI arguments.
+ *
+ * See .claude/hooks/hook-bridge.sh for the implementation.
  */
 function generateHooksConfig(config: HooksConfig): object {
   const hooks: Record<string, unknown[]> = {};
 
-  // PreToolUse hooks - cross-platform via npx with defensive guards
+  // PreToolUse hooks - use hook-bridge.sh to parse stdin JSON
   if (config.preToolUse) {
     hooks.PreToolUse = [
       // File edit hooks with intelligence routing
@@ -156,7 +162,7 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$TOOL_INPUT_file_path" ] && npx @claude-flow/cli@latest hooks pre-edit --file "$TOOL_INPUT_file_path" 2>/dev/null || true',
+            command: '.claude/hooks/hook-bridge.sh pre-edit',
             timeout: config.timeout,
             continueOnError: true,
           },
@@ -168,19 +174,19 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$TOOL_INPUT_command" ] && npx @claude-flow/cli@latest hooks pre-command --command "$TOOL_INPUT_command" 2>/dev/null || true',
+            command: '.claude/hooks/hook-bridge.sh pre-command',
             timeout: config.timeout,
             continueOnError: true,
           },
         ],
       },
-      // Task/Agent hooks - require task-id for tracking
+      // Task/Agent hooks
       {
         matcher: '^Task$',
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$TOOL_INPUT_prompt" ] && npx @claude-flow/cli@latest hooks pre-task --task-id "task-$(date +%s)" --description "$TOOL_INPUT_prompt" 2>/dev/null || true',
+            command: '.claude/hooks/hook-bridge.sh pre-task',
             timeout: config.timeout,
             continueOnError: true,
           },
@@ -189,7 +195,7 @@ function generateHooksConfig(config: HooksConfig): object {
     ];
   }
 
-  // PostToolUse hooks - cross-platform via npx with defensive guards
+  // PostToolUse hooks - use hook-bridge.sh to parse stdin JSON
   if (config.postToolUse) {
     hooks.PostToolUse = [
       // File edit hooks with neural pattern training
@@ -198,7 +204,7 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$TOOL_INPUT_file_path" ] && npx @claude-flow/cli@latest hooks post-edit --file "$TOOL_INPUT_file_path" --success "${TOOL_SUCCESS:-true}" 2>/dev/null || true',
+            command: '.claude/hooks/hook-bridge.sh post-edit',
             timeout: config.timeout,
             continueOnError: true,
           },
@@ -210,19 +216,19 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$TOOL_INPUT_command" ] && npx @claude-flow/cli@latest hooks post-command --command "$TOOL_INPUT_command" --success "${TOOL_SUCCESS:-true}" 2>/dev/null || true',
+            command: '.claude/hooks/hook-bridge.sh post-command',
             timeout: config.timeout,
             continueOnError: true,
           },
         ],
       },
-      // Task completion hooks - use task-id
+      // Task completion hooks
       {
         matcher: '^Task$',
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$TOOL_RESULT_agent_id" ] && npx @claude-flow/cli@latest hooks post-task --task-id "$TOOL_RESULT_agent_id" --success "${TOOL_SUCCESS:-true}" 2>/dev/null || true',
+            command: '.claude/hooks/hook-bridge.sh post-task',
             timeout: config.timeout,
             continueOnError: true,
           },
@@ -238,7 +244,7 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$PROMPT" ] && npx @claude-flow/cli@latest hooks route --task "$PROMPT" || true',
+            command: '.claude/hooks/hook-bridge.sh route',
             timeout: config.timeout,
             continueOnError: true,
           },
@@ -254,14 +260,14 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: 'npx @claude-flow/cli@latest daemon start --quiet 2>/dev/null || true',
-            timeout: 5000,
+            command: '.claude/hooks/hook-bridge.sh daemon-start',
+            timeout: 10000,
             continueOnError: true,
           },
           {
             type: 'command',
-            command: '[ -n "$SESSION_ID" ] && npx @claude-flow/cli@latest hooks session-restore --session-id "$SESSION_ID" 2>/dev/null || true',
-            timeout: 10000,
+            command: '.claude/hooks/hook-bridge.sh session-restore',
+            timeout: 15000,
             continueOnError: true,
           },
         ],
@@ -270,14 +276,13 @@ function generateHooksConfig(config: HooksConfig): object {
   }
 
   // Stop hooks for task evaluation - always return ok by default
-  // The hook outputs JSON that Claude Code validates
   if (config.stop) {
     hooks.Stop = [
       {
         hooks: [
           {
             type: 'command',
-            command: 'echo \'{"ok": true}\'',
+            command: '.claude/hooks/hook-bridge.sh stop-check',
             timeout: 1000,
           },
         ],
@@ -292,8 +297,8 @@ function generateHooksConfig(config: HooksConfig): object {
         hooks: [
           {
             type: 'command',
-            command: '[ -n "$NOTIFICATION_MESSAGE" ] && npx @claude-flow/cli@latest memory store --namespace notifications --key "notify-$(date +%s)" --value "$NOTIFICATION_MESSAGE" 2>/dev/null || true',
-            timeout: 3000,
+            command: '.claude/hooks/hook-bridge.sh notify',
+            timeout: 5000,
             continueOnError: true,
           },
         ],