Discharging cheese production wastewater with high concentrations of organics and nutrients is detrimental to receiving aquatic systems, as the release of these deleterious substances cause oxygen depletion, and eutrophication respectively. On-site treatment of cheese production wastewater requires the removal of high concentrations of organics and nutrients with a small land footprint to meet regulations. There is therefore a critical need for compact, high-rate, cost-effective wastewater technologies such a as the moving bed biofilm reactor (MBBR). Although MBBR systems have been well established for carbon and nitrogen removal, to date only a limited number of studies have achieved enhanced biological phosphorous removal in sequencing batch moving bed biofilm reactor (SB-MBBR) systems, and only for municipal-strength wastewater. Operating SB-MBBR systems under sequencing batch mode enables the reactor operation to be well synced to the fluctuating influent concentrations and flow characteristics of cheese production wastewaters. Furthermore, cycling between anaerobic and aerobic conditions can be achieved in a single sequencing batch reactor, which can promote the proliferation of poly-phosphate accumulating organisms. The SB-MBBR is studied in this research for the removal of carbon, nitrogen, and phosphorous from cheese production wastewaters. Specifically, the effects of anaerobic staging time, aeration rate, enhanced aerobic operation, and adding a second reactor in series was studied by analyzing the kinetics, biofilm characteristics, and microbiome. Extending the anaerobic staging time was shown to achieve aerobic soluble chemical oxygen demand removal rates of 92.5±2.8 g·m⁻²d⁻¹, by selecting for a thinner biofilm with, with a lower biofilm dry-density and a more rough biofilm surface, and therefore likely a biofilm with an enhanced mass transport. A significant shift in the microbiome was observed with longer anaerobic staging times and lower aeration, whereby possible putative poly-phosphate accumulating organisms including Brachymonas, and Dechloromonas were selected for in greater relative abundances compared to anaerobic bacteria. The total phosphorous removal in the possibly resulted from enhanced biological phosphorous removal, supported by the high abundance of putative poly-phosphate accumulating organisms (43.1±8.4%), which dominated the biofilms in the SB-MBBRs with 120 and 168 minute anaerobic staging times. Finally, total ammonia nitrogen oxidation was achieved through partial nitritation with a two reactor in series configuration with a removal rate of 1.07±0.05 g-N·m⁻²d⁻¹. Two SB-MBBRs operated in series was shown to be the superior strategy for achieving TAN compared to a single SB-MBBR with extended aerobic operation. By operating two SB-MBBRs in series, competition between autotrophic nitrifiers and heterotrophs is averted, and AOB proliferate in the biofilm, achieving TAN oxidation. Since TAN oxidation is likely achieved through partial nitrification, the SB-MBBR technology may be incorporated in a deammonification treatment train. The overall study presents novel information for the SB-MBBR design and operation, along with biofilm and microbiome fundamental findings that will guide future pilot- and full-scale applications of the SB-MBBR to treat cheese production wastewater.