In this paper, a novel framework is proposed for integrating biomimetic-based advanced control and multi-agent optimization approaches for nonlinear chemical process applications. In particular, a Biologically-Inspired Optimal Control Strategy, denoted as BIO-CS, is combined with multi-agent optimization (MAO) techniques to provide optimal solutions for dynamic systems. In this combined framework, the BIO-CS algorithm employs gradient-based optimal control solvers for the intermediate problems associated with the leader-follower agents' local interactions. Also, the MAO uses the capabilities of heuristic based optimization techniques by sharing process information to obtain optimal operating setpoints for the controller considering an overall process objective. The applicability of the proposed method is demonstrated using a nonlinear, multivariable, process model of a fermentation system. Specifically, the optimal operating points are computed by the MAO implementation for setpoint tracking, trajectory tracking and plant-model mismatch scenarios for BIO-CS application. Results of the developed framework are compared to a gradient-based Sequential Quadratic Programming (SQP) technique and a classical proportional-integral (PI) controller in terms of optimization and control studies, respectively. As an additional contribution, BIO-CS is also cast as a model predictive controller (MPC) for the first time and compared to the agent-based BIO-CS approach in terms of computational time and tracking error. Closed-loop control results show up to 46% improvement in tracking performance during transient for the multi-agent BIO-CS when compared to BIO-CS as MPC for additional computational expense. The obtained results illustrate the capabilities of this novel integrated framework including BIO-CS as MPC to achieve desired nonlinear system performance for various scenarios. (C) 2018 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.