After upgrading to OS X Yosemite, you might encounter a problem where your Mac appears to always boot in Safe Mode, a maintenance boot environment where OS X only loads minimal and essential system services, in addition to running a few system checking routines. In general this mode is invoked purposefully by holding the Shift key down at boot; however, there are times when the system will automatically be triggered into Safe Mode.

If you suspect this latter occurrence is what is happening to your Mac, then there are a couple of things to consider.

Is it really booting to Safe Mode?

Characteristic of older versions of OS X was a progress bar that would display when you hold the Shift key down to get into Safe Mode. This is still the same in OS X Yosemite; however, in addition Apple has changed the classing spinning wheel icon to a thin progress bar. Therefore, when booting normally in Yosemite you should expect to see a progress bar. In addition, when your Mac loads the login window, you will see “Safe Mode” in red text on the upper-right of the screen.

Reset the PRAM

When you hold the Shift key to boot into Safe Mode, you are passing a boot variable to OS X. Your Mac can also store this variable in a hardware storage chip called the PRAM (parameter RAM) so the Shift key does not have to be held down. If this is occurring, then you can try fixing the issue by resetting your PRAM. To do this, reboot your Mac and then hold down the Option-Command-P-R keys together when you hear the boot chimes. Wait for the system to reset and sound the boot chimes once more, and then release the keys and allow it to boot normally.

Fix or format your Hard Drive

Another possible reason why your Mac is booting to Safe Mode is that your boot drive is experiencing deep formatting problems. If OS X detects such problems with your drive, then it may be spurred into Safe Mode when you boot. Therefore, try restarting your Mac into Recovery Mode by holding Command-R keys when you hear the boot chimes. Then at the OS X Tools menu, select Disk Utility and use this to run a First Aid verification on your boot volume and on the disk device itself (the item listed above your boot drive’s name). This will check the partition schemes and drive formatting. If any problems are found, then use Disk Utility to fix them, followed by restarting your Mac to test whether this has fixed the problem.

If your Mac is still only booting into Safe Mode, then finally consider formatting your hard drive and restoring your system from a Time Machine backup. To do this, first ensure you have a full backup of your system, and then again restart into Recovery Mode. In here, use Disk Utility to select your hard drive device and then use the Partition tab that appears, to partition and format your drive. To do this, select “1 Partition” from the drop-down menu, and then below this click the Options button. In here, ensure GUID is set as the partition type, and then click OK. Next, give the drive a name and select Mac OS Extended (Journaled) as the format type. Then proceed with formatting.

When finished, quit Disk Utility and use the option to restore your Mac from Time Machine Backup to restore your system.

Cannot format or partition your drive?

There may be times when your drive is experiencing corruption that prevents it from being formatted by Disk Utility. You might get an error that states the drive device is busy, cannot be unmounted, or similar. If this occurs, then you will need to boot to a completely different device instead of the drive, format it, and then restore OS X to it.

There are several approaches you can take for this, but one is to install OS X on a spare external USB hard drive, and then boot your Mac to this drive. From here, you should be able to use Disk Utility in a similar way as mentioned above to access your Mac’s internal drive, and format it. Following this, you can reboot your Mac into Internet Recovery mode (hold Option-Command-R down when you hear the boot chimes), and then again use the option here to Restore your Mac from your Time Machine backup.

This should result in a cleanly partitioned and formatted hard drive that has your OS X installation, programs, settings, accounts, and data files all restored to it properly, and the system should now boot normally.