A significant challenge in the rational design of organic thermoelectric materials is to realize simultaneously high electrical conductivity and high induced-voltage in response to a thermal gradient, which is represented by the Seebeck coefficient. Conventional wisdom posits that the polymer alone dictates thermoelectric efficiency. Herein, we show that doping — in particular, clustering of dopants within conjugated polymer films — has a profound and predictable influence on their thermoelectric properties. We correlate Seebeck coefficient and electrical conductivity of iodine-doped poly(3-hexylthiophene) and poly[2,5-bis(2-octyldodecyl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione-3,6-diyl)-alt-(2,2′;5′,2′′;5′′,2′′′-quaterthiophen-5,5′′′-diyl)] films with Kelvin probe force microscopy to highlight the role of the spatial distribution of dopants in determining overall charge transport. We fit the experimental data to a phonon-assisted hopping model and found that the distribution of dopants alters the distribution of the density of states and the Kang–Snyder transport parameter. These results highlight the importance of controlling dopant distribution within conjugated polymer films for thermoelectric and other electronic applications.