Anammox-mediated systems are thought to be cost-effective and efficient technologies for removing nitrogen from wastewater by converting nitrite and ammonium into dinitrogen gas. However, there are inhibitory substances that reduce the effectiveness and efficiency of these processes, preventing their widespread application. Antimicrobial agents are among these substances that have been observed to inhibit anammox-mediated processes. Therefore, this review provides a comprehensive overview of the effects of various antimicrobials on the anammox-based systems with emphasis on the effects in different reactor configurations, sludge types and microbial population of anammox-based systems. In addition, this review also discusses the mechanisms by which nitrifying bacteria are inhibited by the antimicrobials. Gaps in knowledge based on this review as well as future research needs have also been suggested. This review gives a better knowledge of antimicrobial effects on anammox-based systems and provides some guidance on the type of system to use to treat antimicrobial-containing wastewater using anammox-based processes.