At present, microalgae based biodiesel is difficult to commercialize because of its high production costs compared with petroleum resources. This dissertation aims to improve the economic feasibility of microalgae resources by co-producing biodiesel and a high value-added product, omega-3 fatty acid esters. The nutrients required for microalgae cultivation were provided by cheese whey, which is a byproduct of the cheese-making process, enhancing the growth and productivity of the biomass and lipids. After cultivation of the microalgae with cheese whey, separate discrete processes, including lipid extraction, conversion, and recovery, were integrated to simplify the entire downstream process. To increase the efficiency of the integrated process, carbonate, which is a by-product of the electrochemical system used to capture the greenhouse gas CO2, was applied as a catalyst. The amount of organic solvents needed to recover the final product was minimized, and finally, a bio-solvent, which does not contain toxic substances, was used to produce carbon neutral, eco-friendly, and economical biodiesel, plus omega-3 fatty acid esters.