Soybean oil deodorizer distillate (SODD) was enzymatically modified to obtain a product mixture comprised mainly of sterol esters, tocopherols, and fatty acid ethyl esters. Firstly, the original SODD was mixed with oleic acid to reduce its melting point from 65–70 to 30–35 °C and also to produce a reaction mixture with a ratio of free fatty acids (FFA) to sterols close to 2 to improve the progress of sterols esterification. Two enzymatic steps were used in order to separate sterols esterification and ethyl esterification in time and space. The first enzymatic step (in the presence of Candida rugosa lipase) allowed to efficiently transform more than 90% of the original sterols in a short period of time (5 h). The second enzymatic step (in the presence of Novozym 435) converted more than 95% of the FFA in less than 3 h. In addition, the stability of both biocatalysts has been evaluated and both bioprocesses have been scaled-up reutilizing the same batch of lipase up to 8 and 3 times for the first and the second enzymatic step, respectively. The final product obtained is intended to be used as starting material for the purification of sterol esters, tocopherols, and fatty acid ethyl esters via supercritical fluid extraction.