Extracellular electron transfer (EET) by sulfate-reducing bacteria (SRB), such as Desulfovibrio ferrophilus IS5, enables bacterial interactions with minerals, which are vital for biogeochemical cycling and environmental chemistry. Here, we explore the direct EET mechanisms through outer-membrane cytochromes (OMCs) using IS5 as a model SRB. We employed nanostructured electrodes arrayed with 0, 50, 200, and 500 nm long nanowires (NWs) coated with indium–tin–doped oxide to examine the impact of electrode morphology on the direct EET efficacy. Compared to flat electrodes, NW electrodes significantly enhanced current production in IS5 with OMCs. However, this enhancement was diminished when OMC expression was reduced. Differential pulse voltammetry revealed that NW electrodes specifically augmented redox peaks associated with OMCs without affecting those related to redox mediators, suggesting that NWs foster direct EET through OMCs. Scanning electron microscopy observations following electrochemical analyses revealed a novel vertical cell attachment and aggregation on NW electrodes, contrasting with the horizontal monolayer cell attachment on flat electrodes. This study presents the first evidence of the critical role of electrode nanoscale topography in modulating SRB cell orientation and aggregation behavior. The findings underscore the significant influence of electrode morphology on the direct EET kinetics, highlighting the potential impact of mineral morphology on mineral reduction and biogeochemical processes.