An apparatus to facilitate enabling secure state-clean during configuration of partial reconfiguration bitstreams on accelerator devices is disclosed. The apparatus includes a security engine to receive an incoming partial reconfiguration (PR) bitstream corresponding to a new PR persona to configure a region of the apparatus; perform, as part of a PR configuration sequence for the new PR persona, a first clear operation to clear previously-set persona configuration bits in the region; perform, as part of the PR configuration sequence subsequent to the first clear operation, a set operation to set new persona configuration bits in the region; and perform, as part of the PR configuration sequence, a second clear operation to clear memory blocks of the region that became unfrozen subsequent to the set operation, the second clear operation performed using a persona-dependent mask corresponding to the new PR persona.