This research explores the design of cultivation strategies for a microalgal system, which will enable production of selected products based on economic value and market size. The microalgae are cultivated under heterotrophic conditions, which involves a nutrient feed of organic carbon substrate, to prevent light dependency. Glucose yields high cell density and lipid content for biofuel production from Auxenochlorella protothecoides under nitrogen-deplete conditions but leads to chloroplast bleaching. Hence, waste streams from the biodiesel industry, in the form of glycerol, are incorporated in the batch level system in order to modulate the pigment content. The glycerol rich conditions enabled production of significantly high levels of lutein and beta-carotene at about 52.43 mg.L-1 and 6.2 mg.L-1 respectively. High biomass growth of 11.53 g.L-1 was reported for C:N ratio of 10:1 in glucose rich conditions. Since distinct nutrients promote accumulation of specific products, a mathematical model is used to simulate and predict micro-algal response to varying cultivation conditions in the batch level operation. For a reliable model, the biochemical reactions within the micro-algae are reconstructed and calibrated to predict the performance results for varying nutrient conditions. The mathematical model enables scale-up and control of process conditions within the bioreactor system. A sustainable and feasible solution for a micro-algal production system strengthens the bio-economy and renewable energy sector.