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 perform, as part of a PR configuration sequence for a new partial reconfiguration (PR) persona corresponding to a PR bitstream, 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.