Systems and methods for virtual machine data replication with shared resources. An example method may include: identifying resources that are shared across a plurality of virtual machines, storing a copy of the resources, receiving, an indication of a portion of virtual storage of a virtual machine to be replicated, determining that the portion of virtual storage is not included in the resources, in response to the determination, updating a replicated copy of the virtual machine in view of the portion of virtual storage, the replicated copy further including the resources that are shared across a plurality of virtual machines, determining an initialization efficiency metric in relation to the replicated copy, and in response to the determination that the initialization efficiency metric exceeds an efficiency threshold, storing a copy of the virtual storage.