One issue with the large-scale production of microalgae-based biofuels is microbial contamination of microalgal growth reactors. We therefore studied whether reactor growth conditions could be engineered to improve the growth of oleaginous (i.e., lipid-rich) microalgal concentrations in mixed-culture reactors. Scenedesmus dimorphus is an oleaginous microalga that outgrows other microalgae under high CO2 concentrations. Therefore, our goal was to determine if elevated CO2 concentrations, compared to ambient air, could be used to maintain the abundance of S. dimorphus in a mixed culture over time. We grew S. dimorphus together with wild microalgae and bacteria collected from a wastewater effluent stream in modified sequential batch photobioreactors for nine, one-week growth cycles. We used next-generation sequencing and qPCR to quantitatively track the composition of the microbial population within the reactors over time. The results show that elevated CO2 concentrations did lead to improved microalgal growth and higher S. dimorphus concentrations in later growth cycles.