Oleaginous yeasts are microbial factories capable of converting carbohydrates and fat substrates into lipids. The transesterification of these lipids results in the production of biodiesel, a renewable energy source that has emerged as a promising and sustainable alternative to overcome the eminent depletion of fossil fuels and to reduce the environmental impacts of petroleum exploitation. To bring biodiesel production as a realistic technology to respond to the worldwide energy demand, process optimization is to be pursued. In this paper, we performed a model-based optimization of lipid productivity in continuous mode operation. It is considered that two input flow rates at different carbon/nitrogen ratio are available as manipulated variables. The optimal control problem was solved numerically by using the control vector parameterization approach. A simple parameterization with piecewise linear functions was found to be suitable for providing optimal performances. We showed that by driving the carbon/nitrogen ratio along the process adequately, optimal performances are attained. The control strategy here developed excels substantially an operation with a single input flow rate with fixed C/N ratio. This work sets up useful guidelines towards optimal bioprocesses for microbial lipid production.