After I quit the Messages application, I will still receive my iMessages on my Mac. I don't want to disable my iMessages completely but I'd like them to stop bothering me when I've closed the application.
Way to stop receiving iMessages on OS X when the Messages application is closed
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An update for Mac OS X 10.9 (Mavericks). You can turn on Do Not Disturb in Notification Centre to mute notifications:
You can show Notification Centre by clicking on the three-horizontal-lines icon on the far-right of the menubar, or perhaps by doing a two-finger swipe from the right edge of your trackpad (if this gesture is enabled in System Preferences -> Trackpad -> More Gestures). Then swipe up to reveal the 'Do Not Disturb' toggle (which is hidden at the top of the notification centre panel).
Update: I've also just discovered that you can option-click on the Notification centre menubar icon to toggle Do Not Disturb mode on and off.
Silly answer: don't touch it. Sensible answer: presume you are not wanting to send read receipts until you are ready? If so, note that it should return you to the same view you left it in, so to avoid this have a new conversation to a blank sender and select this conversation before minimising/quitting.
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Best Answer
Yes, you can achieve your desired behavior without disabling Messages on your Mac.
If you turn off notifications for Messages from within System Preferences, you will still receive the messages, but will not be notified that they came in.
You can turn notifications off on the following screen. Simply click on "None", and deselect all the checkboxes, as illustrated below: