Electrically conducting polymers are interesting for applications ranging from thermoelectrics to chemical and biological sensing. Recently, thermal transport in polymers has received significant attention as very high and very low thermal conductivity polymers have been reported. The microstructure, including alignment and crystallinity, of the polymer chains significantly impacts the thermal and electrical transport. This work examines how controlling the microstructure through varying deposition conditions can yield tunable material properties for specific organic electronic applications. In this work, we measure both the thermal conductivity of microdots of electrodeposited polypyrrole using the 3ω technique and the electrical conductivity of the polymer. The effects of deposition parameters are examined to determine the optimal deposition conditions.