The high conductivity of initially solvent-doped poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) thin films is reduced unexpectedly upon immersion in sulfuric acid, forming a new morphology type introduced as a “patchy” grain morphology. Correlating the intra-grain structural parameters and grain morphology via spectroscopy and atomic force microscopy quantification and using a comprehensive 3D crystalline structural model, it is revealed that the slow PEDOT interchain charge transport, dictated by the π–π stacking distance and abundance within each grain, is the primary factor controlling the overall conductivity, while the grain morphology has a weaker influence.