A method for producing biofuels is provided. A method of making biofuels includes dewatering substantially intact algal cells to make an algal biomass, sequentially adding solvent sets to the algal biomass, and sequentially separating solid biomass fractions from liquid fractions to arrive at a liquid fraction comprising neutral lipids. The method also includes esterifying the neutral lipids, separating a water miscible fraction comprising glycerin from a water immiscible fraction comprising fuel esters, carotenoids, and omega-3 fatty acids. The method also includes obtaining a C16 or shorter fuel esters fraction, a C16 or longer fuel ester fraction, and a residue comprising carotenoids and omega-3 fatty acids. The method includes hydrogenating and deoxygenating at least one of (i) the C16 or shorter fuel esters to obtain a jet fuel blend stock and (ii) the C16 or longer fuel esters to obtain a diesel blend stock.