We adsorbed fluorinated-alkyl (FmSAM) and hydrogenated-alkyl (HmSAM) phosphonic acids with different molecular lengths on anodes of bulk-heterojunction polymer solar cells. We found the fill factors and series resistances of devices having FmSAMs to more steeply depend on molecular length than those having HmSAMs. We attribute this phenomenon to the smaller tunneling decay factor of HmSAM compared to FmSAM, which is consistent with DFT calculations that reveal differences in the extents of electron density localization of the highest occupied molecular orbitals of these species.