In this study, a synthetic dairy effluent (SDE) containing high levels of COD and nitrogen was treated in a fixed-bed bioreactor (FBBR) under the influence of the variations in residence time, aeration conditions and temperature. The tests performed continuously in a single step and the same reaction vessel allowed to define a 96 h cycle comprising two anoxic/aerobic phases of 48 h each. Sequential anoxic and aerobic conditions improved the removal of TKN and NH4+ by a factor of 2.5, whereas low temperature (10–15 °C) significantly decreased the nitrogen and COD removal rate. Overall, outcomes showed a successful growth of the biomass that reached (5.8 ± 0.31) × 106 CFU/mL, and high removal efficiency of COD (93.5 ± 8.1%), NO3− (99.2 ± 19%), TKN (87.5 ± 16.1%), and NH4+ (55.8 ± 8.3%), and hence complied with Moroccan standards. The FBBR system, therefore, can be applied successfully to remove COD and nitrogen from wastewater.