ATP synthase is central to biological energy conversion, synthesising the majority of cellular ATP. This function is achieved by coupling proton translocation across biological membranes with a rotary catalytic mechanism. Here we describe multiple cryo-EM structures of the detergent solubilised bacterial F1Fo-ATP synthase in three distinct rotor positions. The models not only reveal novel structural features not found in other rotary ATPases, but also provide strong evidence for the proton translocation and autoinhibitory mechanisms proposed for this enzyme.