Conductive polymers have been increasingly used as fuel cell catalyst support due to their electrical conductivity, large surface areas and stability. The incorporation of metal nanoparticles into a polymer matrix can effectively increase the specific surface area of these materials and hence improve the catalytic efficiency. In this work, a nanoparticle loaded conductive polymer nanocomposite was obtained by a one-step synthesis approach based on room temperature direct current plasma-liquid interaction. Gold nanoparticles were directly synthesized from HAuCl4 precursor in poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS). The resulting AuNPs/PEDOT:PSS nanocomposites were subsequently characterized under a practical alkaline direct ethanol fuel cell operation condition for its potential application as an electrocatalyst. Results show that AuNPs sizes within the PEDOT:PSS matrix are dependent on the plasma treatment time and precursor concentration, which in turn affect the nanocomposites electrical conductivity and their catalytic performance. Under certain synthesis conditions, unique nanoscale AuNPs/PEDOT:PSS core-shell structures could also be produced, indicating the interaction at the AuNPs/polymer interface. The enhanced catalytic activity shown by AuNPs/PEDOT:PSS has been attributed to the effective electron transfer and reactive species diffusion through the porous polymer network, as well as the synergistic interfacial interaction at the metal/polymer and metal/metal interfaces.