The focus on renewable energy is increasing globally to lessen reliance on conventional sources and fossil fuels. For renewable energy systems to work at their best and produce the desired results, precise feedback control is required. Microbial electrochemical cells (MEC) are a relatively new technology for renewable energy. In this study, we design and implement a model-based robust controller for a continuous MEC reactor. We compare its performance with those of traditional methods involving a proportional integral derivative (PID), H-infinity (H∞) controller and PID controller tuned by intelligent genetic algorithms. Recently, a dynamic model of a MEC continuous reactor was proposed, which describes the complex dynamics of MEC through a set of nonlinear differential equations. Until now, no model-based control approaches for MEC have been proposed. For optimal and robust output control of a continuous-reactor MEC system, we linearize the model to state a linear time-invariant (LTI) state-space representation at the nominal operating point. The LTI model is used to design four different types of controllers. The designed controllers and systems are simulated, and their performances are evaluated and compared for various operating conditions. Our findings show that a structured linear fractional transformation (LFT)-based H∞ control approach is much better than the other approaches against various performance parameters. The study provides numerous possibilities for control applications of continuous MEC reactor processes.