The anaerobic ammonium oxidation (anammox) process is well-known as a low-energy consuming and eco-friendly technology for treating nitrogen-rich wastewater. Although the anammox reaction was widely investigated in terms of its application in many wastewater treatment processes, practical anammox application at the pilot and industrial scales is limited because nitrogen removal efficiency and anammox activity are dependent on many operational factors such as temperature, pH, dissolved oxygen concentration, nitrogen loading, and organic matter content. In practical application, anammox bacteria are possibly vulnerable to non-essential compounds such as sulfides, toxic metal elements, alcohols, phenols, and antibiotics that are potential inhibitors owing to the complexity of the wastewater stream. This review systematically summarizes up-to-date studies on the effect of various operational factors on nitrogen removal performance along with reactor type, mode of operation (batch or continuous), and cultured anammox bacterial species. The effect of potential anammox inhibition factors such as high nitrite concentration, high salinity, sulfides, toxic metal elements, and toxic organic compounds is listed with a thorough interpretation of the synergistic and antagonistic toxicity of these inhibitors. Finally, the strategy for optimization of anammox processes for wastewater treatment is suggested, and the importance of future studies on anammox applications is indicated.