The development of new materials for microorganism immobilization is very important in wastewater treatment. In this work polyurethane (PU) foams were modified polymerizing pyrrole and aniline onto their surface by chemical oxidization to obtain polyurethane/polypyrrole (PU/PPy), polyurethane/polyaniline (PU/PANI), and PU/(PPy‐co‐PANI) supports which were used to immobilize microorganisms for municipal wastewater treatment in batch mode and continuous flow using two sequential (anaerobic/aerobic) packed bed reactors (PBR) varying the total hydraulic retention time (HRT). The supports were characterized by Fourier Transform Infrared (FTIR) spectroscopy and Scanning Electron Microscopy (SEM) and tested in chemical oxygen demand (COD) removal during treatment of a municipal wastewater. It was observed from SEM analysis that globular nanostructures of PPy and PPy‐co‐PANI were formed onto the PU surface with average diameters between 100 and 300 nm, which are typical of aqueous polymerization of pyrrole monomer; however irregular nanostructures were observed when PANI was homopolymerized onto the PU foam. Batch wastewater treatment after 14 days showed COD removal efficiencies of 77%, 69%, 78%, and 80% for PU foam, PU/PPy, PU/PANI, and PU/(PPy‐co‐PANI), respectively; which was explained as a function of polymers morphology deposited onto the PU foam surface. Also it was observed from the sequential PBR that for 24 h and 36 h of HRT, 80 and 90% of COD removal can be achieved; respectively.© 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2015, 132, 42242.