Through comparing autistic and non-autistic adults in learning and recognizing masked faces, we found that although autistic participants generally had poorer face recognition performance than matched controls, the two groups were similarly impaired by mask use. Nevertheless, when viewing masked faces during learning, they showed reduced tendency to look at the eyes and reduced change in eye movement consistency as compared with controls; this was not observed during recognition. Across participants, selective attention ability and flexibility to change face scanning behavior according to mask conditions were two important factors accounting for individual differences in performance. Interestingly, autistic spectrum quotient accounted for additional variance when recognizing masked faces learned also with a mask, suggesting additional influence from one's autistic traits that could have impacted face learning experience during development. Our findings have important implications for identifying vulnerable populations whose face recognition ability may be particularly affected by mask use.