Abstract: In the renewable energy generation, several processes require the integration of a set of advanced techniques in order to find optimal solutions. Dynamic estimation, stabilizing control for disturbance rejection, optimization for control effort, and parameter tuning are techniques used to address the whole process requirements and obtain optimal results. In this paper, an optimal control strategy for a maximum biofuel production in the presence of disturbances is proposed. First, an integrated optimal control strategy to maximize biofuel production in the presence of disturbances is proposed. Second, due to its high nonlinearity, complex nature, and multiplicity of equilibrium points, a biological process for biofuel generation is described in order to demonstrate the efficiency of the optimal control strategy. A nonlinear discrete-time neural observer for unknown nonlinear systems in the presence of external disturbances and parameter uncertainties is used to estimate unmeasurable variables. An inverse optimal control law for trajectory tracking based on the neural observer is designed such that asymptotic convergence reference trajectory is guaranteed. Differential Evolution and Clonal Selection Algorithms are used to calculate the optimal parameters for neural network training, neural network gains, and feedback control gains. Additionally, a supervisory fuzzy control is proposed in order to select the adequate control action between the closed loop and the open loop and to determine optimal reference trajectories. Simulation results comparison and statistical validation are presented, where it is demonstrated that the optimal control strategy integrated with the Differential Evolution algorithm gives better results to maximize the biofuel production in the presence of disturbances.