Conducting polymer polyelectrolyte microspheres are typically composed of a cationic conducting polymer and an anionic polymer. The polymer chains inside these microspheres are physically or chemically cross-linked, creating a network that enables high water retention. Poly(3,4-ethylenedioxythiophene) (PEDOT) being an electrically conductive polymer exhibits a high conductivity and has great biotechnological applications. The unique combination of properties of PEDOT containing polyelectrolyte microspheres makes them widely investigated materials for electroresponsive cells, tissue engineering, and bio-sensors. The demand to produce PEDOT with varied properties depending the specific application requires the understanding of the basic principles of template formation. In the present work, we studied the inverse suspension polymerization of p-styrenesulfonic acid in the presence of a cross-linking agent as a synthetic way for the formation of porous polyelectrolyte microspheres. We traced how the nature of the emulsifier affected both the structure of the surface layer of the microspheres and the degree of their cross-linking. The porous structure of polyelectrolyte microspheres obtained is found to promote the polymerization of EDOT in their presence throughout the entire microsphere volume. The structural characteristics of the polyelectrolyte/PEDOT complexes in relation to their electrochemical properties have been studied.