Nowadays, energy management environment is a very important issue that technologies have focused on in order to save costs and minimize energy waste. This objective can be achieved by means of an energy resource management approach through an appropriate optimization technique. However, energy savings can conflict with other objective functions, to solve the problem a multi-objective optimization that considers the minimization of the control energy can be adopted. In this paper, we propose to use a multi-objective indirect neural adaptive control concept for nonlinear systems with unknown dynamics. The control scheme consists of an adaptive instantaneous neural emulator and neural controller built on fully connected real-time recurrent learning networks (RTRL). The multi-objective particle swarm optimization (MOPSO) algorithm is used as a mechanism to find NE and NC adaptive learning rates that optimize the proposed objective functions: control energy minimization and closed-loop preservation. Comparative studies and experimental validation on a semi-batch reactor, used to generate cleaner biofuels, are performed to confirm the effectiveness of the proposed strategy.