Extensive studies have focused on improving the operational stability of perovskite solar cells, but few have surveyed the fundamental degradation mechanisms. One aspect overlooked in earlier works is the effect of the atmosphere on device performance during operation. Here we investigate the degradation mechanisms of perovskite solar cells operated under vacuum and under a nitrogen atmosphere using synchrotron radiation-based operando grazing-incidence X-ray scattering methods. Unlike the observations described in previous reports, we find that light-induced phase segregation, lattice shrinkage and morphology deformation occur under vacuum. Under nitrogen, only lattice shrinkage appears during the operation of solar cells, resulting in better device stability. The different behaviour under nitrogen is attributed to a larger energy barrier for lattice distortion and phase segregation. Finally, we find that the migration of excessive PbI2 to the interface between the perovskite and the hole transport layer degrades the performance of devices under vacuum or under nitrogen. Understanding degradation mechanisms in perovskite solar cells is key to their development. Now, Guo et al. show a greater degradation of the perovskite structure and morphology for devices operated under vacuum than under nitrogen.