Investigations on the impact of interfacial modification on organic optoelectronic device performance often attribute the improved device performance to the optoelectronic properties of the modifier. A critical assumption of such conclusions is that the organic active layer deposited on top of the modified surface (interface) remains unaltered. Here the validity of this assumption is investigated by examining the impact of substrate surface properties on the morphology of poly(3-hexylthiophene):1-(3-methoxycarbonyl)-propyl-1-phenyl-[6,6]C61 (P3HT:PCBM) bulk-heterojunction (BHJ). A set of four nickel oxide and poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) hole transport layers (HTL) with contrasting surface properties and performance in organic photovoltaic (OPV) devices is studied. Differences in vertical composition variation and structural morphologies are observed across the samples, but only in the near-interface region of <∼20 nm. Near-interface differences in morphology are most closely correlated with surface polarity and surface roughness of the HTL. Surface polarity is more influenced by surface composition than surface roughness and crystal structure. These findings corroborate the previously mentioned conclusions that the differences in device performance observed in solar cells employing these HTLs are dominated by the electronic properties of the HTL/organic photoactive active layer interface and not by unintentional alteration in the BHJ active layer morphology.