The effect of thermal treatment on the structure and electrical/optical properties of vapor phase-polymerized poly(3,4-ethylenedioxythiophene):tosylate (PEDOT:Tos) and polypyrrole:tosylate (PPy:Tos) polymer films was investigated. Thermal treatment was applied postpolymerization but prior to washing the embedded oxidant layer out of the polymer film. Structural and chemical changes arising from the treatment were studied in the context of their conductive and electrochromic behavior. Spectroscopic analysis indicated a rise in the doping levels of both conductive polymers when exposed to thermal treatment. Additionally, an increase in the film thickness was recorded after the oxidant and other unbound species were removed from the polymer layer using an ethanol rinse. As such, a strong indication that polymerization continued even in the absence of (external) monomer vapor was present. This film thickness increase was most pronounced for PPy:Tos but also present in the PEDOT:Tos film. Heat-treated films exhibited enhanced cohesion, making them more robust and therefore increasing the viability for the material to be used in the optoelectronics area. This robustness, due to additional (cross-linking) oligomer growth, came at the expense of lower conductivity relative to their untreated counterparts.