The food and beverage industry produces wastewaters containing high concentrations of organic carbon and nutrients, which when discharged leads to eutrophication and algal blooms. Given recent stringencies in effluent regulations, industries are required to treat their wastewater on-site. There is a critical need for compact, high-rate, cost-effective wastewater technologies to treat industrial wastewaters, such as the sequencing batch moving bed biofilm reactor. The aim of this study is to investigate the potential and evaluate the performance of the sequencing batch moving bed biofilm reactor cycling between anaerobic and aerobic stages to treat high-strength food and beverage wastewaters. Specifically, this study focuses on the effects of anaerobic staging times and enhanced aeration on the removal of carbon, nitrogen, and phosphorous from cheese production wastewaters. Increasing anaerobic staging times was found to improve the removal rates of carbon beyond previously reported moving bed biofilm reactor results. Increasing the anaerobic stage however decreased the total nitrogen removal, with organic nitrogen undergoing ammonification during the anaerobic stage. This study demonstrates an optimum anaerobic staging time of 138 min; with a carbon removal rate of 31.1 g-sCOD·m−2d−1 and a nitrogen removal rate of 1.3 g-N·m−2d−1. Enhanced aeration was found to be detrimental to phosphorous removal, where a moderate aeration rate demonstrated a net total phosphorous removal of approximately 22 mg-P·l−1 with the phosphorous-content of the suspended solids being approximately 4%. Finally, the sequencing batch moving bed biofilm reactor shows potential for on-site treatment of carbon, nitrogen, and phosphorous from cheese production wastewater.