Abstract Government regulations require on-site treatment of industrial wastewater prior to sewage discharge to prevent environmental degradation of receiving waterbodies. The sequencing batch moving bed biofilm reactor (SB-MBBR) can permit on-site treatment of high organic and nutrient content of cheese production wastewater. However, the critical challenge exists of maintaining both an active heterotrophic and an autotrophic population in a single biofilm system treating carbon and ammonia to low discharge levels from cheese production wastewater. Two SB-MBBRs in series separate the heterotrophic and autotrophic communities, circumventing the competition between the heterotrophic and autotrophic populations in a single biofilm system treating wastewater with high carbon to nitrogen ratios. The first reactor (AN/AE) was operated by cycling between anaerobic and aerobic stages to select for polyphosphate accumulating organisms, and the AN/AE reactor degraded carbon and phosphorous. The second reactor (NIT) was operated with aerobic conditions to promote nitrifying bacteria and treat total ammonia nitrogen. The performance of this system for carbonaceous constituents and ammonia was evaluated by quantifying the kinetics, biofilm morphology, thickness, dry-mass, and dry-density of the two SB-MBBR in series technology. The AN/AE reactor achieved 97.5 ± 1.7%, 58.8 ± 5%, and 49 ± 1% soluble chemical oxygen demand, total nitrogen, and total phosphorous removal efficiencies respectively. The NIT reactor achieved 98.7 ± 2.4 % total ammonia nitrogen removal, though partial nitritation at rates of 1.09 ± 0.03 g-N·m-2d-1, indicating this system can be incorporated in an anammox system. The study demonstrates that enhanced biological phosphorous removal, and potentially anaerobic removal of ammonia can be achieved for on-site treatment of cheese production wastewater.