The Complete Guide to an OS X Clean Install of macOS Sierra

Apple has designed OS X/macOS so that one can just upgrade to the next version, "over the top," seamlessly. With this kind of upgrade, all user data, settings and accounts remain as before, and that works for most users most times. However, there are occasions when a user needs to do what's called a "Clean Install." This is like setting up a Mac as if it first came out of the box and then personal data is restored. This article, after a brief introduction, will list the steps needed for that Clean Install.

There are some users who suspect that a Clean Install is a good way to approach a complete new version of OS X or macOS. Over time, a lot of cruft, that is, unused extensions, app support files, preferences and other files in your Library folder or System Library folder can become troublesome or even a security issue, like Java. Or just take up too much space. See, for example: "How to Manage the Secret Software That Google Chrome Installs on Your Mac."

In addition, sometimes the normal housecleaning process with apps like Spring Cleaning and App Zapper can't solve a particularly difficult issue, and the only way to get a fresh start is a Clean Install.

But First, Let Me Talk You Out of Doing This

A Clean Install, as you'll see below, can be a time intensive process. On the other hand, over the years, we've learned that OS X is pretty good about ignoring things that are no longer applicable. For example, in OS X Yosemite, unless a kernel extension is digitally signed by Apple it won't load.

Adam Christianson (@MacCast) has written "If you aren’t really having any issues or problems then just download the new OS, install over the top and go on your merry way."

We both agree that an over the top is generally the best idea. Those who still pursue the thought of a Clean Install usually reconsider when they realize that everything they own will be deleted from the Mac.

  • The boot drive is erased.
  • All user accounts are deleted.
  • All the files in all the user accounts (spouse, children, family cat) will be deleted. Every document, movie, song and photo will be deleted.
  • All network settings are deleted.
  • Every application and its license files will be gone.

Forging Ahead

However, there is a way to do a Clean Install and restore all your data if you really want to. That's what this article is all about. In summary, you will:

  • Make thorough backups of your entire boot drive in several ways.
  • Erase your boot drive.
  • Install OS X El Capitan (or macOS Sierra)
  • Restore your network settings, user accounts and all data. That means email, photos, music...everything.

I suggest you read this entire article first, understanding all the steps before you begin. Steps #5 and #6 require some preparation, are particularly tricky and must be handled with care. Ready? Here we go!

The Clean Install Process

Step #1. Prepare and Verify. Disconnect any unnecessary peripherals such as printers, tablets, microphones, etc. Try to work with just attached drives and a wired mouse and keyboard. Identify which items are backed up to iCloud. System Preferences > iCloud.

Use Disk Utility to make sure your boot drive permissions are all repaired and that the disk directory is verified as good. This will make sure your Time Machine backup doesn't get scrambled. Then you're ready for the next step.

Step #2. Backups. I recommend two methods.

Time Machine. Do one last Time Machine backup. (Menu Bar > Time Machine > Backup Now.) Later, if you have a curent Time Machine backup and something goes very wrong, you can boot from the recovery partition (CMD-R) and do a complete erase (Disk Utility) and then restore from your Time Machine archive. You'll be back where you were before you started.

File by file with Carbon Copy Cloner. This is a preferred tool by many for making an exact copy of your boot drive to an external Hard Disk Drive (HDD) or Solid State Drive (SSD). That way, you can always mount that external drive, access and copy over individual files.


2.1 You may want to have a log of all your application licenses in a copyable format so that when you restore your apps, you'll have this information handy and can paste it in. I use BBEdit.

2.2 If you try to take a short cut and just copy back in your Library folder, to make licensing easier, you'll be defeating the idea of a Clean Install. That's because the personal Library folder is one place that typically needs a thorough housecleaning.

2.3 Take note of all your mission critical apps and make sure they're all compatible with El Capitan. A great resource for that is Barring sufficient information there, you'll have to visit the developer's website.

2.4 Some simple apps can be copied back to the Applications folder in El Capitan and run just fine. Others will require an installer that places supporting files on your Mac in various places, for example, your personal Library folder.

Catalog these apps so that you'll know which ones came from the Mac App Store and can be readily recovered and those which require you to download a new installer from the developer's website.

2.5 Note that Carbon Copy Cloner takes care of accounts on your Mac other than your own. For example, your spouse. Dont forget those!

Next page: Steps #3 to #7: Download, Install and Restore.

Page 2: Download, Install, Restore


Step #3. Go to the Apple Menu > App Store... and download the El Capitan installer. It will be placed in your Applications folder with the name: "Install OS X El," and it will auto launch. Immediately quit (CMD-Q) out of the upgrade process and move this file from Applications to somehere else, say, a Flash drive. It's about 6 gigabytes.

Step #4. Boot from the recovery partition and use Disk Utility to repartition the Mac's main boot drive. Name the partition something meaningful, select the HFS journaled option for the partition and use the Advanced Option to select GUID. That makes an Intel Mac drive bootable.

Step #5. Ahead of time, prepare a bootable USB Flash drive with El Capitan on it. Follow these steps in a great Macworld article by Dan Frakes: "How to make a bootable OS X 10.11 El Capitan installer drive." Note, you'll need an app called DiskMaker to complete that procedure.   Alternatively, Apple has a note on an alternative process to create a bootable Flash drive. Install OS X El Capitan on the internal drive and reboot the Mac.

Step #6. Rebuilding Your Apps & Data. Right after you boot El Capitan the setup process will start. Here's where it gets tricky, and you have two options.

Step #6a. This is a simpler option, but violates the spirit of a pure Clean Install. You can elect to restore user accounts and settings from Time Machine. One good set of restore options is as follows:

  • Users folder - Yes
  • Applications - No
  • Settings - Yes
  • Other files and folders - Yes

Then restore your apps. By the way, Menu Bar items will be in you own account, but also be aware of System wide device drivers, for example, mouse or trackpad drivers. For the apps, you'll probably have a mix of Mac App Store apps and apps directly from the developer. Here's where that list you made comes in handy.


Step #6b. Elect to start all over with the restoration of your applications, documents, and drivers.

Keep in mind that this can be a relatively tedious option because you may have all your email, photos and music in quasi-OS X databases such as Mail App, (or others), Photos or iTunes and a manual restore of the supporting files requires you to know how they're structured, where they are and how to pull them back in. This will be time consuming, error prone and require experience. Also note that you'll be rebuilding your keychain and password keeper, like 1Password, if you use it.

No matter which option you chose, 6a or 6b, when you sign into iCloud, things like your mail (after you rebuild or log in to your account), calendar, contacts, reminders, Safari bookmarks, etc, will sync up if you had previously selected those items in iCloud sync. If you elected to have an iCloud keychain, it will sync up as well.

Step #7. If you can afford it, make a fresh set of backups to brand new external drives. If you run into a problem, Murphy's Laws dictate that it'll be right after you overwrite your backups. If that's not possible, wait for quite awhile to be sure everything is all good, then redo your file backups on the drive you first used.

When you attach your Time Machine drive, it should ask if you want to use this disk and if you want it to pick up from the old Time Machine data (Recommendation: say Yes). Then you'll have a before and after TM archive.

Wrap up

This process is an art form for an experienced user. Careful, wise decisions will result in a clean install of El Capitan that has all your personal data and settings restored. Solid backups will ensure that if something goes wrong or you need to back out of the procedure, you can revert to where you were with Time Machine—in addition to having Finder accessible copies of every file on your Mac.

A clean Install is a lot of work, but it may be the only recourse in some difficult cases. For the vast majority of users, a simple "over the top" upgrade will be preferable, easier, faster and less error prone. And OS X will likely be just as fast.