A moving bed biofilm reactor with pre-denitrification configuration was fed with a synthetic wastewater containing high chemical oxygen demand (COD) and ammonia. By changing different variables including ammonium and COD loading, nitrification rate in the aerobic reactor and denitrification rate in the anoxic reactor were monitored. Changing the influent loading was achieved via adjusting the inlet COD (956–2,096 mg/L), inlet ammonium (183–438 mg/L), and hydraulic retention time of the aerobic reactor (8, 12, and 18 hours). The overall organic loading rate was in the range of 3.60–17.37 gCOD/m2·day, of which 18.5–91% was removed in the anoxic reactor depending on the operational conditions. Considering the complementary role of the aerobic reactor, the overall COD removal was in the range 87.3–98.8%. In addition, nitrification rate increased with influent ammonium loading, the maximum rate reaching 3.05 gNH4/m2·day. One of the most important factors affecting nitrification rate was influent C:N entering the aerobic reactor, by increasing which nitrification rate decreased asymptotically. Nitrate removal efficiency in the anoxic reactor was also controlled by the inlet nitrate level entering the anoxic reactor. Furthermore, by increasing the nitrate loading rate from 0.91 to 3.49 gNO/m3·day, denitrification rate increased from 0.496 to 2.47 gNO/m3·day.