How to do a clean install of OS X El Capitan on your Mac

“Apple has designed OS X so that one can just upgrade to the next version, ‘over the top,’ seamlessly,” John Martellaro writes for The Mac Observer.

“With this kind of upgrade, all user data, settings and accounts remain as before, and that works for most users most times,” Martellaro writes. “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.”

“There are some users who suspect that a Clean Install is a good way to approach a complete new version of OS X. 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,” Martellaro writes. “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.”

“The Complete Guide to an OS X Clean Install of El Capitan” is here.

MacDailyNews Take: There’s nothing like a clean install – except for a new Mac!


  1. I tried for hours to do a clean install, but it would never finish the first ‘preparing to install’ part. It would get down to one second remaining and that’s it (many tries, many downloads of the installer, many times remaking the memory stick, etc.). Finally had to install the whole OS on an SD card, then boot up, create an account and run the installer from there. That worked.

    1. It is a lot of work, but it’s the only way to really clean things out. I probably had a couple dozen or so things installed that I never used anymore just laying around taking up space and periodically checking for updates and doing who knows what else. As much as I can I keep an up to date copy of every program I install, so I have just about everything I need to get back up and running. The hardest thing is dealing with all of the different ways programs have of reentering the license info. There are so MANY different ways. And email. Restoring email just gets worse every time.

  2. This is why I got so frustrated with Apple when they stopped shipping install disc or being able to buy and install disc. I like to do clean installs for many reason both work related and good computer hygene. With an install disc doing a clean install is drop dead simple.

    1. You guys are blowing this out of proportion.

      You could download El Capitan, create a USB installer, format the internal drive and start an install before you could even get to the Apple Store to pick up a disk copy of an OS.

      The article linked above is long because it goes into detail about backing up your data prior to wiping your drive. All of those same steps are required even with a disk copy (if you value your data).

      1. Which version of OS X is installed by OS X Recovery?
        If you use the Recovery System stored on your startup drive to reinstall OS X, it installs the most recent version of OS X previously installed on this computer.
        If you use Internet Recovery to reinstall OS X, it installs the version of OS X that originally came with your computer. After installation is finished, use the Mac App Store to install related updates or later versions of OS X that you have previously purchased.

        The other thing to take into account, is that you are not doing a “clean install” unless you first use Disk Utility to erase or zero and erase the boot drive. If you don’t do this you will simply be reinstalling the OS. The user data/applications etc. will still remain on the drive.

        The bottom line is an internet recovery is not the way to do a “clean install” of El Capitan if upgrading your OS.

        Feel free to correct me if I’m wrong.

  3. I think that the terminology is a bit wrong here. A “Clean Install” in Apple OS terms, is when the installer software installs the new system software as a totally new write to the “disk” and wraps the old version which it is replacing, in its own folder – usually renaming it as “old system”.
    The new system is fresh with no possibility of contamination from any dross that may be lurking in the old files and the old version can be trashed. there is no need to remove the user data. However, backups are always advised regardless of how the new OS is installed.
    Apple stopped offering this “clean install” option many years ago and presumably devised an installation process to overcome the sort of issues that using it were meant to overcome.
    The way to overcome the general computer hygiene issue is to use secure empty trash, especially if you have an SSD as your main drive, however, that option has vanished from the Finder in El Capitan and cannot be found anywhere.

    1. I do not understand your statement regarding secure empty trash. Granted, regular empty trash simply makes that area of your HDD/SSD available for new stuff by clearing the info in the disk file directory. It does not actually erase it. Secure empty trash writes over that area seven times to make the old data unrecoverable (thus “secure”). That is the only difference.

      This is not the primary issue that is addressed by a clean install. Any decent disk maintenance tool can clear data from “deleted” areas on a HDD/SSD. A clean install ensures that only current and necessary system files are present on your computer for the new OS and your existing set of apps (because you have to reinstall them). Over the years, you install and delete apps and upgrade your OS, both of which tend to leave orphaned files on your computer. A clean install will start you out fresh at the expense of some time. Secure empty trash does not address this issue because these files are not in the trash.

      Two more thoughts about secure empty trash. First, it is very slow. It was forced on me at work, and I started scheduling a periodic empty trash at night because it took too long and slowed down HDD access during the work day. Second, it is probably a bad idea for SSDs. Most of them, as I understand it, have a limited number of write cycles per cell. SSDs actually use fancy software to minimize cell rewrites and extend drive life, as well as a certain amount of excess capacity to substitute when others reach end of life. Secure empty trash will eat up your SSD life for nothing, unless you need that security for work.

      A clean install is a powerful, but time consuming step for refreshing your HDD/SSD with a new major release of OS X. Some of the professional HDD cleaners may be able to approximate a clean install by searching out orphaned files for deletion. But I do not use any of them, so I cannot comment on their efficacy. Secure empty trash just writes over blocks that you have designated for deletion. Not the same thing at all.

      1. Otherwise known as erase and install. I only do this when my Mac becomes chronically balky, which does happen from time to time. Erasing the hard disk and reinstalling everything from scratch (without migrating anything) always results in a dramatic improvement in overall performance. I also reinstall just the apps that I use regularly, installing others as the need arises. Since I tend to accumulate many apps over time that I rarely if ever use, I usually end up with a much leaner and meaner startup disk once everything I really need is reinstalled.

    2. Apple says:
       Description: An issue existed in guaranteeing secure deletion of Trash files on some systems, such as those with flash storage. This issue was addressed by removing the “Secure Empty Trash” option.

  4. Would be good if Apple issued an update which removed the junk from previous versions of OS X.

    My restarts and starts after a shut down all take longer than necessary.

    But El Capitan runs very well, Apple did a good job with this one.

    1. The time to restart is driven by the speed of your HDD/SSD, the number of items in your startup folder that load during boot, and your choices (e.g., reopen windows after restart).

      Windows computers had a terrible reputation for building up cruft over time and gradually grinding to a halt. On Windows computers, a wipe and load was almost considered standard, periodic maintenance because of the registry and other factors. I have not had much exposure to Wintel computers since XP, so I do not know if that is still the case. But I have performed many overwrite OS X upgrades on Macs over the years without a problem. Some people just like the freshness of a clean install / wipe and load. But, with OS X, you don’t need to bother unless you are having an unusual problem. Most HDD issues on OS X can be solved with a little disk maintenance and preference edits.

    2. The difficulty is in knowing which files (e.g., libraries) are needed and which are not. Apple knows which core OS files are necessary. But it would be a monumental effort for Apple to attempt to judge the importance of other OS-related files for any given user. Some companies (Microsoft is a key offender) spew files around your HDD, making such a process even more difficult.

      There are HDD cleaner apps that claim to safely get rid of orphaned files and such. Please thoroughly back up your HDD before using one of them. If the HDD cleaner app screws up and deletes one or more necessary files, then you will need to restore back to your prior HDD status.

  5. The hardest thing with a clean install is making sure you have all your app installers and reg codes. With stuff you have had for years things like that go missing.
    Then there are settings files that you would like to keep. Examples are your bookmarks and bookmark folders. If you have a full backup then you should be able to copy over the required settings files if you know where to find them.
    In the end I chickened out and simply did a standard install. El Capitan certainly seems snappier 🙂

    1. Even standard installs fail for the FlexNet license manager; Flexera claims over 3000 software suites using their manager. FlexNet hardcodes the MAC address of en0 into the license file. Apple doesn’t keep the en0 and MAC address mapping static when doing system installs; en0 can get randomly assigned to any hardware ethernet interface available. This combination causes the programs using FlexNet to report a faulty license seemingly randomly; the only fix is to reactivate the software over the net with the original purchase code. This has been a royal pain in the posterior for me during beta cycles with lots of installs.

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