A method of making biofuels, comprising: a. dewatering intact algal cells to make a wet algal biomass comprising intact algal cells; b. combining the wet algal biomass with an amphiphilic solvent set, the solvent set comprising one or more amphiphilic solvents, to make a first extraction mixture, wherein the weight of the amphiphilic solvent set is about the same as the weight of the wet algal biomass; c. separating the first extraction mixture into a first liquid fraction comprising proteins and a first biomass fraction; d. combining the first biomass fraction with an amphiphilic solvent set, the solvent set comprising one or more amphiphilic solvents, to make a second extraction mixture, wherein the weight of the second amphiphilic solvent set is about the same as the weight of the first biomass fraction; e. separating the second extraction mixture into a second liquid fraction comprising polar lipids and a second biomass fraction; f. combining the second biomass fraction with an amphiphilic solvent set, the solvent set comprising one or more amphiphilic solvents, to make a third extraction mixture, wherein the weight of the amphiphilic solvent set is about the same as the weight of the second biomass fraction; g. separating the third extraction mixture into a third liquid fraction comprising neutral lipids and a third biomass fraction, wherein the first liquid fraction has a higher protein concentration than the second and third liquid fractions, the second liquid fraction has a higher polar lipids concentration than the first and third liquid fractions, and the third liquid fraction has a higher neutral lipids concentration than the first and second liquid fractions; h. transesterifying the neutral lipids to produce a mixture comprising glycerin, fuel esters; i. separating a water miscible fraction comprising glycerin from a water immiscible fraction comprising fuel esters; j. recovering the fuel esters. a. dewatering intact algal cells to make a wet algal biomass comprising intact algal cells; b. combining the wet algal biomass with an amphiphilic solvent set, the solvent set comprising one or more amphiphilic solvents, to make a first extraction mixture, wherein the weight of the amphiphilic solvent set is about the same as the weight of the wet algal biomass; c. separating the first extraction mixture into a first liquid fraction comprising proteins and a first biomass fraction; d. combining the first biomass fraction with an amphiphilic solvent set, the solvent set comprising one or more amphiphilic solvents, to make a second extraction mixture, wherein the weight of the second amphiphilic solvent set is about the same as the weight of the first biomass fraction; e. separating the second extraction mixture into a second liquid fraction comprising polar lipids and a second biomass fraction; f. combining the second biomass fraction with an amphiphilic solvent set, the solvent set comprising one or more amphiphilic solvents, to make a third extraction mixture, wherein the weight of the amphiphilic solvent set is about the same as the weight of the second biomass fraction; g. separating the third extraction mixture into a third liquid fraction comprising neutral lipids and a third biomass fraction, wherein the first liquid fraction has a higher protein concentration than the second and third liquid fractions, the second liquid fraction has a higher polar lipids concentration than the first and third liquid fractions, and the third liquid fraction has a higher neutral lipids concentration than the first and second liquid fractions; h. transesterifying the neutral lipids to produce a mixture comprising glycerin, fuel esters; i. separating a water miscible fraction comprising glycerin from a water immiscible fraction comprising fuel esters; j. recovering the fuel esters.