To date, structural superlubricity in microscale contacts is mostly observed in intrinsic graphite flakes that are cleaved by shearing from HOPG mesas in situ or friction pairs assembled in vacuum due to the high requirement of ultra clean interface for superlubricity, which severely limits their practical applications. Herein, we report observations on microscale structural superlubricity in graphite flake pairs assembled under ambient conditions, where contaminants are inevitably present at the interfaces. For such friction pairs, we find a novel running-in phenomenon, where the friction decreases with reciprocating motions, but no morphological or chemical changes can be observed. The underlying mechanism for the new running-in process is revealed to be the removal of third bodies confined between the surfaces. Our results improve the understanding of microscale superlubricity and may help extend the practical applications of superlubricity.