Gilthead sea bream (Sparus aurata) was raised in six individual recirculating aquaculture systems (RAS) whose biofilters’ performance was analyzed. Fish were fed with three different diets (a control diet, a fishmeal-based diet (FM), and a plant meal-based diet (VM)) and with three different feeding strategies (manual feeding to apparent satiation, automatic feeding with restricted ration, and auto-demand feeding). For every combination of diet and feeding strategy, the mean oxygen consumption, ammonia excretion, and ammonia removal rate were determined. Fish fed with the VM diet consumed the most oxygen (20.06?±?1.80 gO₂ consumed kg^?1 day^?1). There were significant differences in ammonia excretion depending on the protein content and protein efficiency of the diet, as well as depending on feeding strategy, which in turn affected ammonia removal rates. Fish fed by auto-demand feeders led to the highest mean ammonia removal rate (0.10 gN-TAN removed m^?2 biofiltration area day^?1), while not leading to peaks of high ammonia concentration in water, which preserve fish welfare and growth.