In this study, we have improved the power factor of conductive polymer nanocomposites by combining layer-by-layer assembly with electrochemical deposition to produce flexible thermoelectric materials based on PEDOT/carbon nanotubes (CNTs)—films. To produce films based on CNTs and PEDOT, a dual approach has been employed: (i) the layer-by-layer method has been utilized for constructing the CNTs layer and (ii) electrochemical polymerization has been used in the synthesis of the conducting polymer. Moreover, the thermoelectric properties were optimized by controlling the experimental conditions including the number of deposition cycles and electropolymerizing time. The electrical characterization of the samples was carried out by measuring the Seebeck voltage produced under a small temperature difference and by measuring the electrical conductivity using the four-point probe method. The resulting values of the Seebeck coefficient S and σ were used to determine the power factor. The structural and morphological analyses of CNTs/PEDOT samples were carried out using scanning electron microscopy (SEM) and Raman spectroscopy. The best power factor achieved was 131.1 (μWm−1K−2), a competitive value comparable to some inorganic thermoelectric materials. Since the synthesis of the CNT/PEDOT layers is rather simple and the ingredients used are relatively inexpensive and environmentally friendly, the proposed nanocomposites are a very interesting approach as an application for recycling heat waste.