This work considers the problem of determining the transition of ethanol-producing bio-reactors from batch to continuous operation and subsequent control subject to constraints and performance considerations. To this end, a Lyapunov-based non-linear model predictive controller is utilized that stabilizes the bio-reactor under continuous mode of operation. The key idea in the predictive controller is the formulation of appropriate stability constraints that allow an explicit characterization of the set of initial conditions from where feasibility of the optimization problem and hence closed-loop stability is guaranteed. Additional constraints are incorporated in the predictive control design to expand on the set of initial conditions that can be stabilized by control designs that only require the value of the Lyapunov function to decay. Then, the explicit characterization of the set of stabilizable initial conditions is used in determining the appropriate time for which the reactor must be run in batch mode. Specifically, the predictive control approach is utilized in determining the appropriate batch length that achieves stabilizable values of the state variables at the end of the batch. Application of the proposed method to the ethanol production process using Zymomonas mobilis as the ethanol producing micro-organism demonstrates the effectiveness of the proposed model predictive control strategy in stabilizing the bio-reactor.