Rational ways of treatment of fecal sludge (FS) from environmentally friendly toilet complexes of railway cars preserved with a biocidal agent (BA) based on quaternary ammonium compounds (QAC) and polyhexamethylene guanidine (PHMG) are considered. The bacteriostatic effect of BA on different groups (aerobic and anaerobic) of microorganisms in preserved FS was shown. An effective method for reducing the toxic effect of BA in FS by means of pretreatment with acid prior to microbiological processing has been proposed. The conditions for carrying out the process were selected, allowing to increase the efficiency of anaerobic fermentation of FS containing BA.