The polythiophene nanoparticles were synthesized with different magnetic flux densities such as 1.5, 2.5 and 4.6 kGauss and also without magnetic field, in an aqueous medium as a green synthesis method. The electrical conductivities and Seebeck coefficients of undoped polythiophene films increased slightly with magnetic flux density. However, electrical conductivities of the samples synthesized in the magnetic field increased considerably by thermal annealing and secondary doping compared to the sample synthesized without magnetic field. The Seebeck coefficients of the samples synthesized with and without magnetic field decreased by thermal annealing and secondary doping. The highest conductivity and power factor were obtained as 476.6 S cm−1 and 43 μW/mK2, respectively, for the polythiophene synthesized with 4.6 kGauss magnetic flux density and then doped with SDS.