You may run into this issue after you’ve perform a system file or database backup using the Magento Backup tools.
Admin -> System -> Configure -> Tools -> Backup
You go to your site and get the dreaded “500 Internal Server error” and nothing will load.
It’s probably due to file permissions issues – somehow they get changed when running the backups and the server cannot handle the new permissions.
Go into your FTP program (ie Filezilla) or PhpMyAdmin File Manager and check the file and directory permissions.
If your folder permissions are higher than 755 and/or your file permissions are higher than 644 for php or 666 for xml files, you’ll need to reset them to restore your site.
There’s also a “Magento Cleanup Script” that can be accessed HERE or a zipped version which can be downloaded HERE . These scripts will change the file permissions and clean up certain directories and caches.
If you’re still having issues after cleaning up all the firectories and files, the next stop should be your system error_log