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Recently, polymers have been attracted great attention because of their thermoelectric materials’ excellent mechanical properties, specifically their cost-effectiveness and scalability at the industrial level. In this study, the electropolymerization conditions (applied potential and deposition time) of PEDOT films were investigated to improve their thermoelectric properties. The morphology and Raman spectroscopy of the PEDOT films were analyzed according to their applied potential and deposition time. The best thermoelectric properties were found in films grown at 1.3 V for 10 min, with an electrical conductivity of 158 ± 8 S/cm, a Seebeck coefficient of 33 ± 1 µV/K, and a power factor of 17 ± 2 µW/K·m2. This power factor value is three times higher than the value reported in the literature for electropolymerized PEDOT films in acetonitrile using lithium perchlorate as a counter-ion. The thermal conductivity was found to be (1.3 ± 0.3) × 10−1 W/m·K. The highest figure of merit obtained at room temperature was (3.9 ± 1.0) × 10−2 using lithium perchlorate as a counter-ion. In addition, three-dimensional (3D) PEDOT nanonetworks were electropolymerized inside 3D anodic aluminum oxide (3D AAO), obtaining lower values in their thermoelectric properties., The authors acknowledge financial support from PID2020-118430GB-I00 and CSIC PIF 2D-MESES. Cristina V. Manzano and Aída Serrano acknowledge funding from Atracción de Talento Investigador de la Comunidad de Madrid, contracts no. 2019-T1/IND-13541 and 2017-t2/IND5395, respectively. O.C.C. acknowledges to micro-TENERGY project from the Ramon Areces’ Foundation. We acknowledge the services of the MiNa Laboratory at IMN and funding from CM (project SpaceTec, S2013/ICE2822), MINECO (project CSIC13-4E-1794) and the EU (FEDER, FSE).