As organic photovoltaic efficiencies steadily improve, understanding degradation pathways becomes increasingly important. In this paper, the stability under prolonged illumination of a prototypical polymer:fullerene active layer is studied without the complications introduced by additional layers and interfaces in complete devices. Combining contactless photoconductivity with spectroscopy, structural characterization at the molecular and film level, and quantum chemical calculations, the mechanism of photoinduced degradation in bulk heterojunctions of poly (3-hexylthiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM) is studied. Bare films are subjected to four conditions for 1000 h with either constant illumination or dark and either ambient or inert atmosphere. All samples are found to be intrinsically stable for 1000+ h under inert conditions, in contrast to complete devices. While PCBM stabilizes P3HT films exposed to air, its fullerene cage is found to undergo a series of oxidations that are responsible for the deterioration of the photoconductivity of the material. Quantum chemical calculations show that PCBM oxides have deeper LUMO levels than pristine PCBM and therefore act as traps for electrons in the PCBM domains.