What's a clean way to stop mongod on Mac OS X?

It's probably because launchctl is managing your mongod instance. If you want to start and shutdown mongod instance, unload that first:

launchctl unload -w ~/Library/LaunchAgents/org.mongodb.mongod.plist

Then start mongod manually:

mongod -f path/to/mongod.conf --fork

You can find your mongod.conf location from ~/Library/LaunchAgents/org.mongodb.mongod.plist.

After that, db.shutdownServer() would work just fine.

Added Feb 22 2014:

If you have mongodb installed via homebrew, homebrew actually has a handy brew services command. To show current running services:

brew services list

To start mongodb:

brew services start mongodb-community

To stop mongodb if it's already running:

brew services stop mongodb-community

Update*

As edufinn pointed out in the comment, brew services is now available as user-defined command and can be installed with following command: brew tap gapple/services.

If you installed mongodb with homebrew, there's an easier way:

List mongo job with launchctl:

launchctl list | grep mongo

Stop mongo job:

launchctl stop <job label>

(For me this is launchctl stop homebrew.mxcl.mongodb)

Start mongo job:

launchctl start <job label>

Simple way is to get the process id of mongodb and kill it. Please note DO NOT USE kill -9 pid for this as it may cause damage to the database.

so, 1. get the pid of mongodb

$ pgrep mongo

you will get pid of mongo, Now

$ kill

You may use kill -15 as well