The ion exchange membrane bioreactor (IEMB) is a particular case of a membrane-supported biofilm reactor, in which oxy-anions, used as electron acceptors by an anoxic mixed microbial culture, are removed from a polluted water stream through an anion-exchange membrane. The opposite side of this membrane is used for the development of a biofilm, contacting a biocompartment, to which nutrients and chloride are fed as a source of "driving" counter-ion. The applicability of a plate-and-frame IEMB module configuration, consisting of a series of membranes, for the treatment of drinking water contaminated with nitrate and perchlorate, was evaluated. Permeation of carbon source across the membrane to the treated water stream was avoided by a dedicated start-up procedure involving a gradual increase of ethanol feeding to the IEMB biocompartment. It was demonstrated that the biocompartment pH must be controlled not only to guarantee a complete perchlorate removal, but also to avoid precipitation of struvite on the membrane surface, which provokes membrane scaling and decreases the availability of nutrients for the biofilm. Under these conditions, the IEMB was successfully operated maintaining both nitrate and perchlorate concentrations in the treated water below their recommended levels for drinking water supplies.