Understanding the nanoscopic chemical and structural changes that drive instabilities in emerging energy materials is essential for mitigating device degradation. The power conversion efficiency of halide perovskite photovoltaic devices has reached 25.7 per cent in single-junction and 29.8 per cent in tandem perovskite/silicon cells1,2, yet retaining such performance under continuous operation has remained elusive3. Here we develop a multimodal microscopy toolkit to reveal that in leading formamidinium-rich perovskite absorbers, nanoscale phase impurities, including hexagonal polytype and lead iodide inclusions, are not only traps for photoexcited carriers, which themselves reduce performance4,5, but also, through the same trapping process, are sites at which photochemical degradation of the absorber layer is seeded. We visualize illumination-induced structural changes at phase impurities associated with trap clusters, revealing that even trace amounts of these phases, otherwise undetected with bulk measurements, compromise device longevity. The type and distribution of these unwanted phase inclusions depends on the film composition and processing, with the presence of polytypes being most detrimental for film photo-stability. Importantly, we reveal that both performance losses and intrinsic degradation processes can be mitigated by modulating these defective phase impurities, and demonstrate that this requires careful tuning of local structural and chemical properties. This multimodal workflow to correlate the nanoscopic landscape of beam-sensitive energy materials will be applicable to a wide range of semiconductors for which a local picture of performance and operational stability has yet to be established.