We studied the influence of different supporting electrolytes (TBAPF6, TMAPF6, TEAPF6, TBAClO4, and LiClO4) on the morphology of PEDOT films electrochemically polymerized on screen-printed carbon electrodes, as part of which the synthesis of gold nanoparticles was tested for the subsequent modification of Ki-67 antibodies. Electrochemical deposition of the polymer was carried out using cyclic voltammetry and was characterized in the same way in solutions without the monomer. The nanoparticles were obtained using chronoamperometry at a constant potential for 3 s. The processes of p- and n-doping/undoping of both deposits (with and without gold) were studied, as was their characterization using SEM and ESEM-EDS. It was found that the supporting electrolytes intervened in the morphology and conductivity of the polymer films. In all films, it was possible to electrosynthesize gold nanoparticles, but the type of supporting electrolyte also influenced their distribution, showing that for this study, the most suitable were those obtained using TBAPF6, giving the most promising results for the covalent modification of antibodies to obtain future biosensors.