The pursuit of fully autotrophic nitrogen removal via the anaerobic ammonium oxidation (anammox) pathway has led to an increased interest in carbon removal technologies, particularly the A-stage of the adsorption/bio-oxidation (A/B) process. The high-rate operation of the A-stage and lack of automatic process control often results in wide variations of chemical oxygen demand (COD) removal that can ultimately impact nitrogen removal in the downstream B-stage process. This study evaluated the use dissolved oxygen (DO) and mixed liquor suspended solids (MLSS) based automatic control strategies through the use of in situ on-line sensors in the A-stage of an A/B pilot study. The objective of using these control strategies was to reduce the variability of COD removal by the A-stage and thus the variability of the effluent C/N. The use of cascade DO control in the A-stage did not impact COD removal at the conditions tested in this study, likely because the bulk DO concentration (>0.5 mg/L) was maintained above the half saturation coefficient of heterotrophic organisms for DO. MLSS-based solids retention time (SRT) control, where MLSS was used as a surrogate for SRT, did not significantly reduce the effluent C/N variability but it was able to reduce COD removal variation in the A-stage by 90%.