When software updates for OS X and apps you have purchased in the App Store become available, by default you will see a message in Notification Center, which you can click to launch the App Store and apply the updates. In the past Apple has offered options to download updates in the background, and install important security updates and app updates, but in Yosemite has included new options that encompass all software updates.
If you go to the App Store system preferences in Yosemite, you will see a new option you can check to “Install OS X Updates.” As with the setting for managing App updates, this is made unavailable until you check the option to download new software updates in the background. When enabled, however, as with the management of App Store updates, this will ensure your operating system software is kept fully up to date.

This new option in the App Store system preferences allows OS X to download and install OS X updates, just as it can for any software updates available for your App Store purchases.
Overall, the options in the App Store system preferences are the following:
- Automatically check for updates — This will only check for software updates and notify you about them, as opposed to doing any automatic downloads and installations.
- Download newly available updates in the background — This will likewise not install any updates, but will make them quicker to install when you are ready, by having them stored on your system instead of needing to be downloaded on-demand from the App Store.
- Install app updates — This will automatically update any App Store applications that you have installed, to ensure they are at the latest versions.
- Install OS X updates — This is the new feature, which will install any OS X updates available from Apple, automatically restarting your system for them to take effect.
- Install system data files and security updates — This will install any critical security updates automatically, to ensure known vulnerabilities and exploits for them are patched.
You might wonder whether or not it is wise to enable any of these features. In most cases, I would recommend against automatic update processes, especially if you use your Mac every day where you will see notifications for any available updates and be able to manage them at your convenience.
The only features in this system preference that I would suggest enabling for your main Mac are the automatic check for updates, and perhaps the option to download newly available updates in the background; however, the others are good options to have and are perhaps best for systems that you might not use all the time, such as system you are using as a local file server, or systems that are part of a computer lab or workgroup. In these instances, you can use these features to keep them as up to date as possible.
Every time there’s an OS X update released we are bombarded by the “this bricked my computer” crowd. Usually, after we get to the bottom of the issues, it turns out that the user had trouble with their system before the update anyway. People do funny things with their machines, configuring them in weird ways, installing questionable software and then forgetting they did, issuing terminal commands they had no business doing. For this segment of users it’s probably best they not enable automatic updates.
While I agree with your conclusions, I don’t often see mea culpas from people who complain about update problems. We may assume the trouble is of their own making but we rarely know this for a fact. Asserting we do is disingenuous.
Another problem, in my opinion, is that people don’t bother with routine system maintenance. This issue is tangential to the one you raise. Trying to install updates, let alone an upgrade, over a secretly ailing system can cause update failure. This is one reason why I don’t install system level updates on my own or on clients’ computers without first using Disk Utility to see that the system is in good condition. If I have time I also run Disk Warrior, which can find problems Disk Utility misses.
As an added precaution with incremental system updates, I use the relevant combo updater. Combo updates replace many more files than an incremental update does and in the process can scotch hidden or even obvious problems.
In sum I agree with Topher that users should oversee updates so that they are in control of the process. This assumes (always a risky thing to do) that the user has a clue about what’s going on. On the other hand, many people decline to install updates when the system makes them available, either because they are busy or because they are actually afraid of the update process. This habit, while understandable, can leave their computer at risk – though given the limited number of OS X exploits in the wild, the risk is not great. Apple’s automatic update options, as with the same function on Windows PCs, is designed to minimize the risk that users will be running a vulnerable machine. Unfortunately, many people don’t know the difference between a legitimate update notice and a possible malware spoof. So they ere on the side of caution. I frequently get calls from clients and friends facing this predicament. In particular, Adobe Flash Player and Adobe Reader receive frequent security updates – and are also sometimes spoofed. So people may be justified in their caution.
Thus there is no one-size-fits-all solution to the update question. One might wish that everyone would be well informed on update issues; unfortunately this is not, nor will it ever be, true.
“If you go to the App Store system preferences in Yosemite” — note that this is App Store in System Preferences, not Preferences in App Store. (Why?)
This is the location of the preferences for the App Store. The program itself does not have built-in preferences settings.
I lost my icon, the second from the left. It suddenly disappeared. I want it back, How?
Thanks Topher! Anybody happen to know where these new “Install OS X updates” are stored before they get installed?