The impact of side-chain variations on the photothermal stability of solar cells containing poly(benzodithiophene–diketopyrrolopyrrole) polymers are investigated in the absence of oxygen. Four different side-chains of benzodithiophene (BDT) are synthesized and copolymerized with diketopyrrolopyrrole (DPP) by Stille polymerization. The photothermal stability is measured as active layer blends with phenyl-C61-butyric acid methyl ester (PCBM) in encapsulated inverted photovoltaic cell architecture with zinc oxide and PEDOT:PSS as transport layers (ITO/ZnO/active layer/PEDOT:PSS/Ag). Device degradation is correlated to the morphological behavior of the polymer:blend upon AM1.5 illumination (UV-visible light, 50 °C) and have been investigated by AFM, XRD, and UV-Vis. Once exposed to the light and to the temperature the BHJ stability is governed by two processes (i) PCBM crystallization and (ii) PCBM dimerization. Dimerization results in a rapid initial performance decrease followed by a more gradual decrease caused by a slower thermally activated crystallization. Depending on the blend morphology, dictated by the polymer's alkyl chain, the two processes occur to different extents thereby modulating the BHJ stability. Thus, of the polymer side-chains explored, linear alkyl side-chains stabilized the bulk heterojunction most effectively followed by no side-chain, alkoxy and branched side-chains. Lowering the concentration of fullerene in the active layer also reduces the rate of degradation across the polymers tested. This is a result of both the rate of crystallization and dimerization of fullerene being dependent on its concentration and the nature of the polymer side-chains. This approach appears to be a general strategy to increase the polymer:PCBM stability.