A method and system for efficiently restoring synthetic full backup based virtual machines that include user checkpoints. Specifically, the method and system disclosed herein overcome a behavioral limitation exhibited in present virtual machine backup methodologies, where said methodologies ignore the presence of user checkpoints storing state for a virtual machine. In accounting for the user checkpoints while recovering a virtual machine, embodiments of the invention maintain restoration points for virtual machine state instantiated by the user, in addition to those instantiated by the system.