Doping of the conjugated polymer poly(3-hexylthiophene) (P3HT) with the p-dopant 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) is a widely used model system for organic thermoelectrics. We here study how the crystalline order influences the Seebeck coefficient of P3HT films doped with F4TCNQ from the vapour phase, which leads to a similar number of F4TCNQ anions and hence (bound + mobile) charge carriers of about 2 × 10⁻⁴ mol cm⁻³. We find that the Seebeck coefficient first slightly increases with the degree of order, but then again decreases for the most crystalline P3HT films. We assign this behaviour to the introduction of new states in the bandgap due to planarisation of polymer chains, and an increase in the number of mobile charge carriers, respectively. Overall, the Seebeck coefficient varies between about 40 to 60 μV K⁻¹. In contrast, the electrical conductivity steadily increases with the degree of order, reaching a value of more than 10 S cm⁻¹, which we explain with the pronounced influence of the semi-crystalline nanostructure on the charge-carrier mobility. Overall, the thermoelectric power factor of F4TCNQ vapour-doped P3HT increases by one order of magnitude, and adopts a value of about 3 μW m⁻¹ K⁻² in the case of the highest degree of crystalline order.