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Updates are necessary, but annoying. Which is why your Mac, by default, installs them automatically.

System updates protect your Mac from malware and other threats, and occasionally add new features. The same goes for software updates, so it's important to keep all your apps up to date. But popups asking users whether they want to install updates have a way of being ignored, even when the user knows that updates are important. So automatic updates make sense for most people.

...But not all people. Some of you prefer having control over what is installed when. Happily, there's a way to take control, and it's in System Preferences.

Click the "App Store" button and you'll see the automatic update settings right at the top of the window.

The first two options are about checking for and downloading updates---not installing them.

  • The top option, "Automatically check for updates," controls whether your Mac regularly checks for new versions or not. There's no good reason to turn this off: it's important to know about updates when they're ready.
  • The next option, "Download newly available updates in the background," controls whether or not you need to tell the system to download updates. The only reason to disable this feature is the need to manage bandwidth usage. If you don't have that need, it's best to leave this enabled.

Again, neither of these options installs updates automatically: they just set whether the system should look for updates regularly, and whether the system should download those updates when available. If you check the above two options, and only those options, you'll still need to tell the system to install updates.

The next three options determine whether your system will install updates without your intervention.

  • Check "Install App updates" and applications you've downloaded using the Mac App Store will install automatically, without you having to do anything. Note that you'll have to close the program in order for the update to install, otherwise you will end up seeing a notification about it.
  • Check "Install macOS updates", and decimal point updates (for example, updating from 10.12.3 to 10.12.4) will install automatically. You will be asked before your system restarts. New versions of macOS (ie, updating from 10.12 Sierra to 10.13 Some-Other-California-Landmark) will not install automatically.
  • Check "install system data files and security updates" to ensure that these regular updates make it to your system. These updates rarely require system reboots, and help keep your Mac secure, so there's no reason not to enable them in our opinion.

There's no right or wrong way to configure all of this: it's all about balancing your tolerance for for pop-ups with your desire to control when and how updates are installed. Most users are probably fine sticking with the default, which for a few years now has been downloading and installing updates automatically.

If you want even more flexibility, consider updating Mac apps from the Terminal. It's a lot faster than opening the App Store, but doesn't require that you trust Apple to install updates automatically.

Why Are Some Apps Still Bugging Me?

These settings only apply to macOS updates and applications downloaded from the Mac App Store, which means that any software you downloaded outside Apple's ecosystem have to handle their own updates. How this works varies from application to application: many will show you a simple notification when an update is available, allowing you to download and install updates in one click.

Anything from Microsoft will require Microsoft Auto-Update (which for some freaking reason always needs to update itself before it can update any software.) There's not much you can do to change this, other than check the settings for individual applications and see if they offer automatic updates. Microsoft offers this feature, for example:

We wish there was one central place to handle all of these third party updates, but so far as we know there isn't, so you'll just have to find these options on a per-app basis. Good luck!