We herein report two different methods to deposit metallic and semiconducting nanoparticles inside a conducting polymer (CP) by controlling the diffusion of an active ion within the film. The first method is a pulsed electrodeposition where the ‘off’ intervals allow the ions to flow into the CPs as they re-oxidize. The second method uses poly(ethylene glycol) (PEG) or ionic liquid (IL) to assist the transportation of the ion within the CP. Pt, Ni, Cu and CdS were successfully deposited inside a conductive film of poly(3,4-ethylenedioxythiophene) (PEDOT) using either of these two methods. Scanning electron microscopy images show that the nanoparticles are well dispersed throughout the films and form open, layered structures in the presence of PEG. Using a phosphonium-based (triisobutylmethylphosphonium tosylate) IL and heat during electrodeposition results in the incorporation of CdS inside a layered polymer scaffold. The presence of the nanoparticles throughout the film is confirmed by EDAX measurements. The PEDOT:PEG–Ni electrodes show electrocatalytic activity towards formate and formic acid oxidation.