This contribution describes a novel process systems engineering framework that couples advanced control with sustainability evaluation for the optimization of process operations to minimize environmental impacts associated with products, materials and energy. The implemented control strategy combines a biologically-inspired method with optimal control concepts for finding more sustainable operating trajectories. The sustainability assessment of process operating points is carried out by using the U.S. EPA’s Gauging Reaction Effectiveness for the ENvironmental Sustainability of Chemistries with a multi-Objective Process Evaluator (GREENSCOPE) tool that provides scores for the selected indicators in the economic, material efficiency, environmental and energy areas. The indicator scores describe process performance on a sustainability measurement scale, effectively determining which operating point is more sustainable if there are more than several steady states for one specific product manufacturing. Through comparisons between a representative benchmark and the optimal steady states obtained through the implementation of the proposed controller, a systematic decision can be made in terms of whether the implementation of the controller is moving the process towards a more sustainable operation. The effectiveness of the proposed framework is illustrated through a case study of a continuous fermentation process for fuel production, whose material and energy time variation models are characterized by multiple steady states and oscillatory conditions.