diff --git a/docs/TROUBLESHOOTING.md b/docs/TROUBLESHOOTING.md
index 0b1bb38..003719e 100644
--- a/docs/TROUBLESHOOTING.md
+++ b/docs/TROUBLESHOOTING.md
@@ -80,13 +80,17 @@ PRODUCTION_DB_HOST=prod.example.com  # Correct: "PRODUCTION" is recognized
 
 3. **Network/firewall restrictions**
    - Check if your database allows remote connections
-   - Verify firewall settings allow connections on the MySQL port (usually 3306)
+   - Verify firewall settings allow connections on the configured MySQL port (`[ENV]_DB_PORT`, default `3306`)
 
 4. **Missing environment variables**
    - Ensure all required variables for your environment are set
    - Run with `DEBUG=true` to see loaded configuration
+
+5. **Incorrect custom port**
+   - If your MySQL server is not on `3306`, set `[ENV]_DB_PORT` explicitly
+   - Ensure the value is a valid integer such as `3307`
    
-5. **Incorrect environment name**
+6. **Incorrect environment name**
    - Verify you're using one of the supported environment names: local, development, staging, production
    - Environment variables must be prefixed with LOCAL_, DEVELOPMENT_, STAGING_, or PRODUCTION_
    - You cannot use custom environment names with this tool (such as DEV_ or PROD_)
@@ -225,4 +229,4 @@ If you can't resolve your issue with this guide:
    - Error messages
    - Steps to reproduce the issue
    - Your environment details (OS, Node.js version)
-   - Debug logs (with sensitive information removed) 
\ No newline at end of file
+   - Debug logs (with sensitive information removed) 
diff --git a/src/db/options.ts b/src/db/options.ts
index 454604a..2963737 100644
--- a/src/db/options.ts
+++ b/src/db/options.ts
@@ -6,14 +6,21 @@ export function getMysqlTimezone(): string {
   return process.env.MYSQL_TIMEZONE || DEFAULT_MYSQL_TIMEZONE;
 }
 
+function getDatabasePort(envPrefix: string): number | undefined {
+  const port = process.env[`${envPrefix}_DB_PORT`];
+  return port ? Number.parseInt(port, 10) : undefined;
+}
+
 export function buildPoolOptions(envPrefix: string): PoolOptions {
+  const sslEnv = process.env[`${envPrefix}_DB_SSL`] ?? process.env.MCP_MYSQL_SSL;
+
   return {
     host: process.env[`${envPrefix}_DB_HOST`],
     user: process.env[`${envPrefix}_DB_USER`],
     password: process.env[`${envPrefix}_DB_PASS`],
     database: process.env[`${envPrefix}_DB_NAME`],
-    port: process.env[`${envPrefix}_DB_PORT`] ? Number(process.env[`${envPrefix}_DB_PORT`]) : undefined,
-    ssl: process.env.MCP_MYSQL_SSL === "true" ? {} : undefined,
+    port: getDatabasePort(envPrefix),
+    ssl: sslEnv === "true" ? {} : undefined,
     connectionLimit: 5,
     enableKeepAlive: true,
     keepAliveInitialDelay: 10000,
diff --git a/src/db/pools.ts b/src/db/pools.ts
index 2d29b7e..0bfc3fa 100644
--- a/src/db/pools.ts
+++ b/src/db/pools.ts
@@ -6,15 +6,9 @@ function debug(message: string, ...args: any[]) {
   process.stderr.write(`DEBUG [Pools]: ${message} ${args.map(arg => JSON.stringify(arg)).join(' ')}\n`);
 }
 
-// Connection pools for each environment
-export const pools = new Map<string, Pool>();
+export const pools = new Map<Environment, Pool>();
+let poolsInitialized = false;
 
-debug('Initializing database pools...');
-debug('Environment enum options:', Object.values(Environment.enum));
-debug('Environment enum type:', typeof Environment);
-debug('Environment enum:', Environment);
-
-// Map of environment to env var prefix
 const ENV_PREFIX_MAP = {
   local: 'LOCAL',
   development: 'DEVELOPMENT',
@@ -22,52 +16,68 @@ const ENV_PREFIX_MAP = {
   production: 'PRODUCTION'
 } as const;
 
-// Initialize pools
-Object.values(Environment.enum).forEach((env) => {
-  const envPrefix = ENV_PREFIX_MAP[env];
-  
-  debug(`=== Initializing pool for ${env} environment ===`);
-  debug(`Using prefix: ${envPrefix}`);
-  debug('Environment variables:');
-  debug(`HOST: ${process.env[`${envPrefix}_DB_HOST`]}`);
-  debug(`USER: ${process.env[`${envPrefix}_DB_USER`]}`);
-  debug(`DB: ${process.env[`${envPrefix}_DB_NAME`]}`);
-  debug(`PASS: ${process.env[`${envPrefix}_DB_PASS`] ? 'set' : 'not set'}`);
-  debug(`SSL: ${process.env.MCP_MYSQL_SSL}`);
-  
-  const config = buildPoolOptions(envPrefix);
+export function initializePools() {
+  if (poolsInitialized) {
+    debug("Pools already initialized");
+    return;
+  }
+
+  debug("Initializing database pools...");
+  debug("Environment enum options:", Object.values(Environment.enum));
+
+  Object.values(Environment.enum).forEach((env) => {
+    const envPrefix = ENV_PREFIX_MAP[env];
+    const config = buildPoolOptions(envPrefix);
+
+    debug(`=== Initializing pool for ${env} environment ===`);
+    debug(`Using prefix: ${envPrefix}`);
+    debug(`HOST: ${process.env[`${envPrefix}_DB_HOST`]}`);
+    debug(`USER: ${process.env[`${envPrefix}_DB_USER`]}`);
+    debug(`DB: ${process.env[`${envPrefix}_DB_NAME`]}`);
+    debug(`PASS: ${process.env[`${envPrefix}_DB_PASS`] ? "set" : "not set"}`);
+    debug(`PORT: ${config.port ?? "default"}`);
+    debug(`SSL: ${process.env[`${envPrefix}_DB_SSL`] ?? process.env.MCP_MYSQL_SSL}`);
+
+    if (config.host && config.user && config.password && config.database) {
+      debug(`Creating pool for ${env} with config:`, {
+        host: config.host,
+        user: config.user,
+        database: config.database,
+        port: config.port ?? 3306,
+        ssl: config.ssl,
+        dateStrings: config.dateStrings,
+        timezone: config.timezone,
+        hasPassword: !!config.password,
+      });
 
-  if (config.host && config.user && config.password && config.database) {
-    debug(`Creating pool for ${env} with config:`, {
-      host: config.host,
-      user: config.user,
-      database: config.database,
-      ssl: config.ssl,
-      dateStrings: config.dateStrings,
-      timezone: config.timezone,
-      hasPassword: !!config.password
-    });
-    
+      try {
+        pools.set(env, createPool(config));
+        debug(`Pool created successfully for ${env}`);
+      } catch (error) {
+        debug(`Error creating pool for ${env}:`, error);
+      }
+    } else {
+      debug(`Missing configuration for ${env}:`, {
+        hasHost: !!config.host,
+        hasUser: !!config.user,
+        hasPass: !!config.password,
+        hasDB: !!config.database,
+      });
+    }
+  });
+
+  poolsInitialized = true;
+  debug("Pools map keys:", Array.from(pools.keys()));
+}
+
+export async function closePools() {
+  for (const [env, pool] of pools.entries()) {
     try {
-      const pool = createPool(config);
-      pools.set(env, pool);
-      debug(`Pool created successfully for ${env}`);
-      debug(`Pool type for ${env}:`, typeof pool);
-      debug(`Pool methods for ${env}:`, Object.keys(pool));
+      debug(`Closing pool for ${env}...`);
+      await pool.end();
+      debug(`Pool for ${env} closed successfully`);
     } catch (error) {
-      debug(`Error creating pool for ${env}:`, error);
+      debug(`Error closing pool for ${env}:`, error);
     }
-  } else {
-    debug(`Missing configuration for ${env}:`, {
-      hasHost: !!config.host,
-      hasUser: !!config.user,
-      hasPass: !!config.password,
-      hasDB: !!config.database
-    });
   }
-});
-
-debug('Final pools state:');
-debug('Pools map keys:', Array.from(pools.keys()));
-debug('Pools map size:', pools.size);
-debug('Pools map entries:', Array.from(pools.entries()).map(([env]) => env));
+}
diff --git a/src/help.ts b/src/help.ts
index bbe7d80..1645b04 100644
--- a/src/help.ts
+++ b/src/help.ts
@@ -21,6 +21,7 @@ Environment Variables:
   LOCAL_DB_USER           Local database username
   LOCAL_DB_PASS           Local database password
   LOCAL_DB_NAME           Local database name
+  LOCAL_DB_PORT           Local database port (default: 3306)
   LOCAL_DB_SSL            Set to 'true' to enable SSL for local database
   
   DEVELOPMENT_DB_*        Development environment database settings
@@ -62,4 +63,4 @@ export function processCommandLineArgs(): void {
   if (process.argv.includes('--version') || process.argv.includes('-v')) {
     showVersion();
   }
-} 
\ No newline at end of file
+} 
diff --git a/src/index.ts b/src/index.ts
index 2c95ee7..49105c2 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -8,7 +8,31 @@ processCommandLineArgs();
 import { config } from "dotenv";
 import { resolve, dirname } from "path";
 import { fileURLToPath } from "url";
-import fs from "fs";
+import { Server } from "@modelcontextprotocol/sdk/server/index.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import {
+  CallToolRequestSchema,
+  ListToolsRequestSchema,
+} from "@modelcontextprotocol/sdk/types.js";
+import { initializePools, closePools } from "./db/pools.js";
+import {
+  queryToolName,
+  queryToolDescription,
+  QueryToolSchema,
+  runQueryTool,
+} from "./tools/query.js";
+import {
+  infoToolName,
+  infoToolDescription,
+  InfoToolSchema,
+  runInfoTool,
+} from "./tools/info.js";
+import {
+  environmentsToolName,
+  environmentsToolDescription,
+  EnvironmentsToolSchema,
+  runEnvironmentsTool,
+} from "./tools/environments.js";
 
 // Get the directory path of the current module
 const __filename = fileURLToPath(import.meta.url);
@@ -39,48 +63,9 @@ debug('Environment variables loaded:', {
   LOCAL_DB_HOST: process.env.LOCAL_DB_HOST,
 });
 
-// Then import pools and MCP server components
-debug('Initializing database pools...');
-import { pools } from "./db/pools.js";
+initializePools();
 
-debug('Importing MCP SDK components...');
-import { Server } from "@modelcontextprotocol/sdk/server/index.js";
-import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
-import {
-  CallToolRequestSchema,
-  ListToolsRequestSchema,
-} from "@modelcontextprotocol/sdk/types.js";
-
-debug('Importing tools...');
-
-debug('Importing query tool...');
-import {
-  queryToolName,
-  queryToolDescription,
-  QueryToolSchema,
-  runQueryTool,
-} from "./tools/query.js";
-debug('Query tool imported:', { queryToolName });
-
-debug('Importing info tool...');
-import {
-  infoToolName,
-  infoToolDescription,
-  InfoToolSchema,
-  runInfoTool,
-} from "./tools/info.js";
-debug('Info tool imported:', { infoToolName });
-
-debug('Importing environments tool...');
-import {
-  environmentsToolName,
-  environmentsToolDescription,
-  EnvironmentsToolSchema,
-  runEnvironmentsTool,
-} from "./tools/environments.js";
-debug('Environments tool imported:', { environmentsToolName });
-
-debug('All tools imported successfully');
+debug('Tools imported successfully');
 
 /**
  * MCP server providing MySQL database tools:
@@ -256,19 +241,8 @@ debug('CallTool handler registered');
 // Handle process termination
 async function cleanup() {
   debug('Starting cleanup...');
-  
-  for (const [env, pool] of pools.entries()) {
-    try {
-      debug(`Closing pool for ${env}...`);
-      await pool.end();
-      debug(`Pool for ${env} closed successfully`);
-    } catch (error) {
-      const message = error instanceof Error ? error.message : "Unknown error";
-      debug(`Error closing pool for ${env}:`, { error, message });
-    }
-  }
-  
-  debug('Cleanup completed');
+  await closePools();
+  debug('Server cleanup completed');
 }
 
 // Clean server startup function matching the PostgreSQL example
diff --git a/src/tools/info.ts b/src/tools/info.ts
index dc4a08f..4fcd492 100644
--- a/src/tools/info.ts
+++ b/src/tools/info.ts
@@ -1,11 +1,7 @@
 import { z } from "zod";
-import { Pool } from "mysql2/promise";
-import { Environment, InfoParams, DatabaseInfo } from "../types/index.js";
-import { config } from "dotenv";
+import { InfoParams, DatabaseInfo } from "../types/index.js";
 import { pools } from "../db/pools.js";
 
-config();
-
 export const infoToolName = "info";
 export const infoToolDescription = "Get information about MySQL databases";
 export const InfoToolSchema = InfoParams;
@@ -70,4 +66,4 @@ export async function runInfoTool(params: z.infer<typeof InfoToolSchema>): Promi
     const message = error instanceof Error ? error.message : "Unknown error occurred";
     throw new Error(`Failed to get database info: ${message}`);
   }
-} 
\ No newline at end of file
+} 
diff --git a/tests/db/pools.test.ts b/tests/db/pools.test.ts
index 2b671cd..266499a 100644
--- a/tests/db/pools.test.ts
+++ b/tests/db/pools.test.ts
@@ -1,11 +1,26 @@
 import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
 import { buildPoolOptions, DEFAULT_MYSQL_TIMEZONE } from '../../src/db/options.js';
 
+const createPool = vi.fn((config) => ({ config }));
+
+vi.mock('mysql2/promise', () => ({
+  createPool,
+}));
+
 describe('database pool options', () => {
   const originalEnv = process.env;
 
   beforeEach(() => {
+    vi.resetModules();
+    vi.clearAllMocks();
     process.env = { ...originalEnv };
+
+    Object.keys(process.env).forEach((key) => {
+      if (key.includes('_DB_') || key.startsWith('MCP_MYSQL_') || key === 'MYSQL_TIMEZONE') {
+        delete process.env[key];
+      }
+    });
+
     vi.spyOn(process.stderr, 'write').mockImplementation(() => true);
   });
 
@@ -33,4 +48,26 @@ describe('database pool options', () => {
 
     expect(options.timezone).toBe('+00:00');
   });
+
+  it('passes a configured custom port to mysql2 pool options', () => {
+    process.env.LOCAL_DB_PORT = '3307';
+
+    const options = buildPoolOptions('LOCAL');
+
+    expect(options.port).toBe(3307);
+  });
+
+  it('does not initialize pools more than once', async () => {
+    process.env.LOCAL_DB_HOST = 'localhost';
+    process.env.LOCAL_DB_USER = 'root';
+    process.env.LOCAL_DB_PASS = 'password';
+    process.env.LOCAL_DB_NAME = 'testdb';
+
+    const { initializePools } = await import('../../src/db/pools.js');
+
+    initializePools();
+    initializePools();
+
+    expect(createPool).toHaveBeenCalledTimes(1);
+  });
 });