The effect of the strong electron acceptor, 2,3,5,6-tetrafluoro-7,7,8,8- tetracyanoquinodimethane (F4-TCNQ), on poly(3-hexylthiophene) (P3HT) aggregates is studied. F4-TCNQ is commonly used as a dopant for P3HT, however, relatively little is currently known about its effect on polymer conformation and packing in the presence of fullerenes. Resonance Raman and optical spectra of pristine P3HT or blends with [6,6]-phenyl-C 61-butyric acid methyl ester (PCBM) doped with F4-TCNQ up to ∼10% w/w show a loss of pristine-type P3HT aggregates with increasing dopant concentration. Complexed P3HT chains possess greater backbone planarity due to hole injection which is corroborated from density functional theory (DFT) calculations of oligothiophene surrogates and F4-TCNQ. Morphologies of doped P3HT/PCBM systems are characterized using scanning transmission electron microscopy (STEM) with electron energy loss spectroscopy (EELS) detection and images reveal mixed clusters of P3HT/F4-TCNQ fibril-like domains that increase in size with dopant loading. The apparent preference of F4-TCNQ for P3HT aggregates is attributed to efficient charge separation stemming owing to the more polarizable nature of chains comprising the aggregate π-stack. © 2013 The Royal Society of Chemistry.