Great progress in the development of new semiconducting polymers over the last two decades alongside improved understanding of electron transport mechanisms have resulted in a dramatic increase in the electron mobility of these materials making them promising candidates for electronic and thermoelectric applications. Heat transport phenomena, on the other hand-which govern thermal conductivity-have not received as much attention up to date. In spite of the simplicity of the principle behind the measurement of thermoelectric properties, the combined uncertainty in thermoelectric figure of merit zT could easily reach 50% with the largest uncertainty coming from thermal conductivity measurements. Such a high measurement uncertainty, often comparable to relative variations in zT encountered when optimizing within a given class of materials, prevents the study of structure-thermal property relationships. Here we present a protocol for the measurement of the thermal conductivity of thin films with reduced measurement uncertainty, which allowed us to investigate the effect of microstructural changes on the thermal conductivity of the conjugated polymer P(NDI2OD-T2). We show that the enhancement of the thermal conductivity upon annealing is much less pronounced than the corresponding increase in the electron mobility that has been reported under the same annealing conditions in the literature. This suggests that semicrystalline conjugated polymers in which thermal transport remains limited by the amorphous domain boundaries in between crystalline grains could be a suitable system for realizing the electron-crystal phonon glass concept and enable higher performance thermoelectric materials.