Conductive polymers, such as polypyrrole (ppy), have been the subject of numerous studies due to their promising applications in organic solar cells, flexible electronics, electrochromic devices, super capacitors, etc. Yet, their application is still limited as a result of poor processability. Silica has been reported to improve the mechanical strength and adhesion of conductive polymer films. In this work, we propose a controllable electrochemical approach for preparing ppy-silica hybrid thin films from a solution containing both pyrrole and silane monomers. It is known that pyrrole can be electropolymerised using anodic potentials, while silica can be electrodeposited under cathodic potentials. Thus, we studied the formation of ppy-silica hybrid thin films on a stainless steel surface by applying alternating potentials, i.e. cathodic followed by anodic pulses (denoted C + A) or anodic followed by cathodic pulses (denoted A + C). We show that by controlling the deposition potential and time for the cathodic and anodic pulses, the film thickness and composition can be manipulated well as analysed using profilometry and EDX. The element depth profile of the films was characterized using secondary ion mass spectroscopy (SIMS). In essence, for the C + A process, pyrrole diffuses through the cathodically electrodeposited wet silica gel layer and undergoes anodic polymerisation on the substrate, while for the A + C process, silane can be electrodeposited both on top of the anodically electrodeposited conductive ppy films as well as on the stainless steel through the pinholes in the ppy film. This offers a simple approach for tuning the structure of conductive polymer-sol-gel composite films.