Optimising the performance of P3HT:PCBM (polymer–fullerene, P3HT – poly(3-hexylthiophene), PCBM – [6, 6]-phenyl-C61-butyric acid methyl ester) blends for solar cell applications is currently impeded by our lack of understanding of the effect of processing conditions on the resulting morphology of P3HT and hence its performance. The literature has generally overlooked studying the link between morphology and tacticity, which, in turn, affects charge mobility. The conformational change from trans to cis between adjacent thiophene rings in the P3HT backbone determines the tacticity of the polymer molecules. We used all-atom molecular dynamics simulations at 400 K, matching typical experimental processing temperatures, to unravel the molecular-level configuration changes that P3HT polymers undergo during processing, focusing here on temperature and shear. The effect of shear was included since it improves charge transport and polymer aggregation in polymer–fullerene blends. Our simulations implicate the side chains in initiating the polymer backbone twisting and curvature that we observe and, consequently, altering the trans-to-cis ratio (and hence mobility). Complementary density functional theory (DFT) calculations indicate that such tacticity conversions follow a rugged energy surface. The simulations also help explain the origin of disorder in the aggregation of polymer chains and shorter conjugation length, all of which are observed in experiments. Each individual polymer molecule’s response to local thermodynamic changes and the kinetics of neighbouring polymers guides its morphological evolution. Thus, we put forward the prominent role of tacticity in determining both kinetic and thermodynamic properties of this prototypical polymer–fullerene blend. As a result, we uncover two types of processing condition effects, one that directly affects polymer conformation (e.g. high temperature), and the other that directly changes the alignment between polymers (e.g. shear).