diff --git a/.changeset/patch-extend-safe-outputs-timeout.md b/.changeset/patch-extend-safe-outputs-timeout.md
new file mode 100644
index 0000000000..56b16e3cb6
--- /dev/null
+++ b/.changeset/patch-extend-safe-outputs-timeout.md
@@ -0,0 +1,5 @@
+---
+"gh-aw": patch
+---
+
+Add more diagnostic logging around safe-outputs MCP server initialization and extend the startup timeout from 10s to 60s to reduce CI flakes.
diff --git a/.changeset/patch-safe-outputs-startup-logging.md b/.changeset/patch-safe-outputs-startup-logging.md
new file mode 100644
index 0000000000..adfb8d2cf0
--- /dev/null
+++ b/.changeset/patch-safe-outputs-startup-logging.md
@@ -0,0 +1,5 @@
+---
+"gh-aw": patch
+---
+
+Add diagnostic logging and widen the safe-outputs MCP server startup timeout to 60 seconds to tame CI flakiness.
diff --git a/actions/setup/js/mcp_http_transport.cjs b/actions/setup/js/mcp_http_transport.cjs
index 9ba0a5336a..044a756b49 100644
--- a/actions/setup/js/mcp_http_transport.cjs
+++ b/actions/setup/js/mcp_http_transport.cjs
@@ -1,6 +1,12 @@
 // @ts-check
 /// <reference types="@actions/github-script" />
 
+const { createLogger } = require("./mcp_logger.cjs");
+const moduleLogger = createLogger("mcp_http_transport");
+
+// Log immediately at module load time
+moduleLogger.debug("Module is being loaded");
+
 /**
  * MCP HTTP Transport Implementation
  *
@@ -74,9 +80,14 @@ class MCPServer {
    * @param {any} transport - Transport instance (must have setServer and start methods)
    */
   async connect(transport) {
+    const logger = createLogger("MCPServer");
+    logger.debug("Starting connect...");
     this.transport = transport;
+    logger.debug("Set transport");
     transport.setServer(this);
+    logger.debug("Called setServer");
     await transport.start();
+    logger.debug("Transport.start() completed");
   }
 
   /**
@@ -126,10 +137,13 @@ class MCPHTTPTransport {
    * Start the transport
    */
   async start() {
+    const logger = createLogger("MCPHTTPTransport");
+    logger.debug(`Called, started=${this.started}`);
     if (this.started) {
       throw new Error("Transport already started");
     }
     this.started = true;
+    logger.debug("Set started=true");
   }
 
   /**
diff --git a/actions/setup/js/mcp_server_core.cjs b/actions/setup/js/mcp_server_core.cjs
index 697ab1d554..e41b6c2067 100644
--- a/actions/setup/js/mcp_server_core.cjs
+++ b/actions/setup/js/mcp_server_core.cjs
@@ -1,6 +1,12 @@
 // @ts-check
 /// <reference types="@actions/github-script" />
 
+const { createLogger } = require("./mcp_logger.cjs");
+const moduleLogger = createLogger("mcp_server_core");
+
+// Log immediately at module load time
+moduleLogger.debug("Module is being loaded");
+
 /**
  * MCP Server Core Module
  *
diff --git a/actions/setup/js/safe-outputs-mcp-server.cjs b/actions/setup/js/safe-outputs-mcp-server.cjs
index 601fbe8f79..decf5dbb13 100644
--- a/actions/setup/js/safe-outputs-mcp-server.cjs
+++ b/actions/setup/js/safe-outputs-mcp-server.cjs
@@ -5,8 +5,16 @@
 // This is the main entry point script for the safe-outputs MCP server
 // It starts the HTTP server on the configured port
 
+const { createLogger } = require("./mcp_logger.cjs");
+const logger = createLogger("safe-outputs-entry");
+
+// Log immediately to verify Node.js execution starts
+logger.debug("Entry point script executing");
+
 const { startHttpServer } = require("./safe_outputs_mcp_server_http.cjs");
 
+logger.debug("Successfully required safe_outputs_mcp_server_http.cjs");
+
 // Start the HTTP server
 // The server reads configuration from /opt/gh-aw/safeoutputs/config.json
 // Port and API key are configured via environment variables:
@@ -18,13 +26,18 @@ const { startHttpServer } = require("./safe_outputs_mcp_server_http.cjs");
 // the MCP gateway doesn't perform the MCP protocol initialization handshake.
 // It directly calls methods like tools/list without the Mcp-Session-Id header.
 if (require.main === module) {
+  logger.debug("In require.main === module block");
   const port = parseInt(process.env.GH_AW_SAFE_OUTPUTS_PORT || "3001", 10);
   const logDir = process.env.GH_AW_MCP_LOG_DIR;
+  logger.debug(`Port: ${port}, LogDir: ${logDir}`);
+  logger.debug("Calling startHttpServer...");
 
   startHttpServer({ port, logDir, stateless: true }).catch(error => {
-    console.error(`Failed to start safe-outputs HTTP server: ${error.message}`);
+    logger.debugError("Failed to start safe-outputs HTTP server: ", error);
     process.exit(1);
   });
+
+  logger.debug("startHttpServer call initiated (async)");
 }
 
 module.exports = { startHttpServer };
diff --git a/actions/setup/js/safe_outputs_mcp_server_http.cjs b/actions/setup/js/safe_outputs_mcp_server_http.cjs
index 873d56ff8c..e4916ac4dd 100644
--- a/actions/setup/js/safe_outputs_mcp_server_http.cjs
+++ b/actions/setup/js/safe_outputs_mcp_server_http.cjs
@@ -1,6 +1,12 @@
 // @ts-check
 /// <reference types="@actions/github-script" />
 
+const { createLogger } = require("./mcp_logger.cjs");
+const moduleLogger = createLogger("safe_outputs_mcp_server_http");
+
+// Log immediately at module load time (before any requires)
+moduleLogger.debug("Module is being loaded");
+
 /**
  * Safe Outputs MCP Server with HTTP Transport
  *
@@ -19,14 +25,23 @@
  */
 
 const http = require("http");
+moduleLogger.debug("Loaded http");
 const { randomUUID } = require("crypto");
+moduleLogger.debug("Loaded crypto");
 const { MCPServer, MCPHTTPTransport } = require("./mcp_http_transport.cjs");
-const { createLogger } = require("./mcp_logger.cjs");
+moduleLogger.debug("Loaded mcp_http_transport.cjs");
+const { createLogger: createMCPLogger } = require("./mcp_logger.cjs");
+moduleLogger.debug("Loaded mcp_logger.cjs");
 const { bootstrapSafeOutputsServer, cleanupConfigFile } = require("./safe_outputs_bootstrap.cjs");
+moduleLogger.debug("Loaded safe_outputs_bootstrap.cjs");
 const { createAppendFunction } = require("./safe_outputs_append.cjs");
+moduleLogger.debug("Loaded safe_outputs_append.cjs");
 const { createHandlers } = require("./safe_outputs_handlers.cjs");
+moduleLogger.debug("Loaded safe_outputs_handlers.cjs");
 const { attachHandlers, registerPredefinedTools, registerDynamicTools } = require("./safe_outputs_tools_loader.cjs");
+moduleLogger.debug("Loaded safe_outputs_tools_loader.cjs");
 const { getErrorMessage } = require("./error_helpers.cjs");
+moduleLogger.debug("All modules loaded successfully");
 
 /**
  * Create and configure the MCP server with tools
@@ -36,7 +51,7 @@ const { getErrorMessage } = require("./error_helpers.cjs");
  */
 function createMCPServer(options = {}) {
   // Create logger early
-  const logger = createLogger("safeoutputs");
+  const logger = createMCPLogger("safeoutputs");
 
   logger.debug(`=== Creating MCP Server ===`);
 
@@ -176,8 +191,9 @@ async function startHttpServer(options = {}) {
   const port = options.port || 3000;
   const stateless = options.stateless || false;
 
-  const logger = createLogger("safe-outputs-startup");
+  const logger = createMCPLogger("safe-outputs-startup");
 
+  logger.debug(`startHttpServer called with port=${port}, stateless=${stateless}`);
   logger.debug(`=== Starting Safe Outputs MCP HTTP Server ===`);
   logger.debug(`Port: ${port}`);
   logger.debug(`Mode: ${stateless ? "stateless" : "stateful"}`);
@@ -185,6 +201,7 @@ async function startHttpServer(options = {}) {
 
   // Create the MCP server
   try {
+    logger.debug(`About to call createMCPServer...`);
     const { server, config, logger: mcpLogger } = createMCPServer({ logDir: options.logDir });
 
     // Use the MCP logger for subsequent messages
@@ -206,7 +223,9 @@ async function startHttpServer(options = {}) {
 
     // Connect server to transport
     logger.debug(`Connecting server to transport...`);
+    logger.debug(`About to call server.connect(transport)...`);
     await server.connect(transport);
+    logger.debug(`server.connect(transport) completed successfully`);
     logger.debug(`Server connected to transport successfully`);
 
     // Create HTTP server
diff --git a/actions/setup/sh/start_safe_outputs_server.sh b/actions/setup/sh/start_safe_outputs_server.sh
index e95cd11cf5..c8fdb5d58c 100755
--- a/actions/setup/sh/start_safe_outputs_server.sh
+++ b/actions/setup/sh/start_safe_outputs_server.sh
@@ -87,9 +87,9 @@ node mcp-server.cjs >> /tmp/gh-aw/mcp-logs/safeoutputs/server.log 2>&1 &
 SERVER_PID=$!
 echo "Started safe-outputs MCP server with PID $SERVER_PID"
 
-# Wait for server to be ready (max 10 seconds)
+# Wait for server to be ready (max 60 seconds)
 echo "Waiting for server to become ready..."
-for i in {1..10}; do
+for i in {1..60}; do
   # Check if process is still running
   if ! kill -0 $SERVER_PID 2>/dev/null; then
     echo "ERROR: Server process $SERVER_PID has died"
@@ -100,12 +100,12 @@ for i in {1..10}; do
   
   # Check if server is responding
   if curl -s -f "http://localhost:$GH_AW_SAFE_OUTPUTS_PORT/health" > /dev/null 2>&1; then
-    echo "Safe Outputs MCP server is ready (attempt $i/10)"
+    echo "Safe Outputs MCP server is ready (attempt $i/60)"
     break
   fi
   
-  if [ "$i" -eq 10 ]; then
-    echo "ERROR: Safe Outputs MCP server failed to start after 10 seconds"
+  if [ "$i" -eq 60 ]; then
+    echo "ERROR: Safe Outputs MCP server failed to start after 60 seconds"
     echo "Process status: $(pgrep -f 'mcp-server.cjs' || echo 'not running')"
     echo "Server log contents:"
     cat /tmp/gh-aw/mcp-logs/safeoutputs/server.log
@@ -114,7 +114,7 @@ for i in {1..10}; do
     exit 1
   fi
   
-  echo "Waiting for server... (attempt $i/10)"
+  echo "Waiting for server... (attempt $i/60)"
   sleep 1
 done