Abstract P3HT:PCBM blends applied as active layers for bulk heterojunction organic solar cells generally show unstable morphologies upon prolonged thermal annealing, severely limiting the lifetime of the devices. As such, the thermodynamic instability of the blend is a limiting factor in the overall performance of organic photovoltaics, and a strong disadvantage in the fierce competition with other photovoltaic technologies. This paper shows whether different blend preparation conditions and intrinsic structural changes in the side chains of poly(3-alkylthiophene) (P3AT) derivatives can influence the thermal stability of the resulting solar cells. A combination of Bright Field Transmission Electron Microscopy (BFTEM) and the analysis of Selected Area Electron Diffraction (SAED) patterns revealed that the investigated preparation conditions do not really affect the thermal stability, whereas the introduction of a small ratio (10%) of specific functional moieties in the side chains of random P3AT copolymers does improve the thermal stability significantly. It was demonstrated that demixing of the blend components upon prolonged thermal annealing is strongly delayed in the functionalized P3AT:PCBM blends. The enhanced thermal stability was confirmed by in-situ monitoring of the short circuit current of organic solar cells based on the respective active layers. The introduction of functionalized side chains hence represents an attractive approach to increase the operational stability of organic photovoltaics based on the bulk heterojunction concept.