Biocidal agents (BAs) are widely used in environmentally safe toilet complexes (ESTC) of passenger railcars to suppress microbial activity in fecal sludge (FS). The subsequent disposal of BA-containing FS at municipal sewage treatment facilities adversely affects their work due to the loss of activated sludge. The antimicrobial properties of BAs based on quaternary ammonium compounds (QAC) and polyhexamethylene guanidine (PHMG), as well as methods for its neutralization, have been studied. It was confirmed that BAs based on QAC and PHMG have an antimicrobial effect on various groups of bacteria, reducing their number by 10-100 or more times. It was found that FS contains two groups of microorganisms with different sensitivities to BA. Methods for the deactivation of BA antimicrobial action in FS were tested with (1) a deactivating agent; (2) incubation with thermophilically digested wastewater sludge as a source of the methanogenic microbial community; and (3) chemical deactivation via acidification or alkalization. The highest efficiency was obtained from thermophilic anaerobic digestion with the pretreatment of FS with a strong acid.