Nanoscale chemical analysis of functional polymer systems by electron microscopy, to gain access into degradation processes during the materials life cycle, is still a formidable challenge due to their beam sensitivity. Here a systematic study on the different stages of degradation in a P3HT-PCBM organic photovoltaic (OPV) model system is presented. To this end pristine samples, samples with (reversibly) physisorbed oxygen and water and samples with (irreversibly) chemisorbed oxygen and water are imaged utilizing the full capabilities of cryogenic STEM-EELS. It is found that oxygen and water are largely physisorbed in this system leading to significant effects on the band structure, especially for PCBM. Quantification proves that degradation concomitantly decreases the amount of C-C bonds and increases the amount of C-O-C bonds in the sample. Finally, it is shown that with a pulsed electron beam utilizing a microwave cavity, beam damage can be significantly reduced which likely extends the possibilities for such studies in future.