Phase I of the proposed energy optimization methodology showed how the selection of best management criteria for the biological aeration process, and the guarantee of its control at the wastewater treatment plant (WWTP) in San Pedro del Pinatar (Murcia, Spain) produced reductions of around 20% in energy consumption by considerably reducing the oxygen needs of the microorganisms in the biological system. This manuscript focused on phase II of this methodology, which describes the tools that can be used to detect and correct deviations in the optimal operating points of the aeration equipment and the intrinsic deficiencies in the installation, in order to achieve optimization of the oxygen needs by the microorganisms and improve the efficiency of their transfer from the gas phase to the liquid phase. The objectives pursued were: (i) to minimize the need for aeration, (ii) to reduce the pressure losses in the installation, (iii) to optimize the air supply pressures to avoid excessive energy consumption for the same airflow, and (iv) to optimize the control strategy for the actual working conditions. The use of flow modeling and simulation techniques, the measurement and calculation of air transfer efficiency through the use of off-gas hoods, and the redesign of the aeration facility at the San Pedro del Pinatar WWTP were crucial, and allowed for reductions in energy consumption in Phase II of more than 20%.