Provided are techniques for encrypting a virtual disk of a virtual computing instance (VCI) while the VCI is online and still running using a mirror driver. In certain aspects a mirror driver is a filter running in an I/O stack used for accessing a virtual disk, such that the mirror driver receives I/Os destined to the virtual disk and mirrors those I/Os to the virtual disk and one or more additional virtual disks. The mirror driver begins copying data from an unencrypted source virtual disk to a destination virtual disk, and the data is encrypted as it is stored in the destination virtual disk, while the VCI is still online. During the copying, as new writes are issued to the unencrypted source virtual disk from the VCI, the mirror driver mirrors the writes to both the unencrypted source virtual disk and the destination virtual disk.