Batteries using fluoride anions as the carrier might possess high capacity and energy density. Especially, the fluoride shuttle battery (FSB), which uses a fluoride-ion-conductive liquid electrolyte and operates at room temperature, has been reported previously and is deemed a solution to the global energy and environmental crises. Although several electrolyte solutions have been synthesized, and the fluorination/defluorination reactions of various active materials have been evaluated, no subsequent FSBs using those electrolyte solutions have been reported. In this study, two metal species, Bi and Pb, which have different fluorination/defluorination mechanisms in the electrolyte solution composed of alkylammonium fluoride and an ionic liquid, were used as the positive and negative active materials for the FSB. The fluorination/defluorination mechanisms at each electrode during the reactions were explained by in situ electrochemical atomic force microscopy (EC-AFM) measurements. Differences in the morphological changes by two existing mechanisms, direct fluorination and dissolution−deposition, were clarified with evidence. Furthermore, the charge/discharge process of the FSB, with the electrolyte solution combining the active materials, was demonstrated, and the cycling performance and capacity fading mechanism were discussed based on the characteristic morphological change of the active materials at their interface with the electrolyte solution obtained by in situ EC-AFM measurements.