The internal recirculation plays an important role in different areas of the biological treatment of wastewater treatment plants because it has a great influence on the concentration of pollutants, especially nutrients. A usual manipulation of the internal recirculation flow rate is based on the target of controlling the nitrate concentration in the last anoxic tank. This work proposes an alternative for the manipulation of the internal recirculation flow rate instead of nitrate control, with the objective of avoiding limit violations of nitrogen and ammonia concentrations and reducing operational costs. A fuzzy controller is proposed to achieve it based on the effects of the internal recirculation flow rate in different areas of the biological treatment. The proposed manipulation of the internal recirculation flow rate is compared to the application of the usual nitrate control in an already established and published operation strategy by using the internationally known benchmark simulation model no. 2 as a working scenario. The results show improvements with reductions of 59.40% in ammonia limit violations, 2.35% in total nitrogen limit violations, and 38% in pumping energy costs.