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% in single junction and 29.8% 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 photo-excited carriers which themselves reduce performance4,5, but via the same trapping process are sites at which photochemical degradation of the absorber layer is seeded. We visualise 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 film composition and processing, with the presence of polytypes being most detrimental for film photo-stability. Importantly, we reveal that performance losses and intrinsic degradation processes can both 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.