Good process control has often been criticized for the economic viability of large-scale production of several commercial products. In this work, the production of biodiesel from microalgae is investigated. Successful implementation of a model-based control strategy requires the identification of a model that properly captures the biochemical dynamics of microalgae, yet is simple enough to allow its implementation for controller design. This paper explores the biodiesel production in a class of continuous culture under heterotrophic conditions via closed-loop operation. A mathematical model adapted from Surisetty et al. (2010) that describe the growth of microalgae in a heterotrophic culture is studied via dynamic analysis. This model is extended to the continuous operation where bifurcation analysis was carried out for the determinate the qualitative model behavior and to analyze feasible operating conditions. This project is focused on the on the use of a mixture of two substrates that are continuously fed into the reactor chamber, and the continuous fermentation process is described by an unstructured mathematical model with a product inhibition on cell growth. In addition, we present the design of a nonlinear control law contains a class of bounded type feedback of the named control error in order to regulate the substrate concentration at maximum value to lead the lipids-diesel concentration indirectly. Lipid productivity in continuous culture was 0.276 g L-1 d-1 via a closed loop (increase of 31.5 %) over that of the continuous mode in open loop. Finally, numerical experiments proved the satisfactory performance of the proposed methodology in comparison with a linear PI controller.