Riboflavin has been proposed to serve as an electron shuttle in photoelectrochemical systems. However, riboflavin was also observed for abiotic photolysis under illumination. Such conflicting reports raise the necessity for further investigation. In this study, riboflavin secreted by Rhodopseudomonas palustris was studied to clarify its stability and electron shuttle function under illumination. The data of high-performance liquid chromatography-mass spectrometry showed that the riboflavin was photolyzed to lumichrome in microbial photoelectrochemical systems. In addition, the anodic current increased by 75% after adding lumichrome compared with that of the control; it further demonstrated that lumichrome, not riboflavin, as an electron shuttle could facilitate microbial electron transfer. This study clarifies the mechanism of the interface process in microbial photoelectrochemical systems.