Soybean oil is extracted by a two-stage process in which up to 85%, preferably from about 60 to about 75%, of the soybean oil in soybeans is extracted by mechanical or solvent extraction to produce first extracted oil and oil-containing meal. The first extracted oil is then refined by caustic or physical refining. Substantially all of the oil remaining in the meal is extracted by solvent extraction to produce second extracted oil and substantially oil-free meal. The second extracted oil may be transesterified for use in biodiesel fuel.