Abstract Microscopy provides a proxy for assessing the operation of perovskite solar cells, yet most works in the literature have focused on bare perovskite thin films, missing charge transport and recombination losses present in full devices. Here we demonstrate a multimodal operando microscopy toolkit to measure and spatially correlate nanoscale charge transport losses, recombination losses and chemical composition. By applying this toolkit to the same scan areas of state-of-the-art, alloyed perovskite cells before and after extended operation, we show that devices with the highest macroscopic performance have the lowest initial performance spatial heterogeneity—a crucial link that is missed in conventional microscopy. We show that engineering stable interfaces is critical to achieving robust devices. Once the interfaces are stabilized, we show that compositional engineering to homogenize charge extraction and to minimize variations in local power conversion efficiency is critical to improve performance and stability. We find that in our device space, perovskites can tolerate spatial disorder in chemistry, but not charge extraction.