The species Yarrowia lipolytica is an aerobic yeast that produces different lipase isoforms, including extracellular, intracellular, and membrane-bound ones. The immobilization of lipases, such as those from Y. lipolytica, increases enzyme stability and lowers operational costs, through its reuse. The characterization of those biocatalysts is highly important to orientate their technological applications. The present work aims to obtain different Y. lipolytica lipases, through fermentation and immobilization techniques, and to evaluate the ester synthesis and hydrolysis activity of these biocatalysts in comparison to a commercial lipase produced by Candida rugosa and test them for phytosterol ester production. High immobilization yield was achieved by microencapsulating Y. lipolytica lipase extract on magnetic nanoparticles (>99.7%). However, immobilization significantly reduced their activity (more than 90%). Lipases from Y. lipolytica showed greater 4-nitrophenyl laurate synthesis in relation to the lipase from C. rugosa. However, C. rugosa lipase was still the best biocatalyst for β-sitosterol oleate synthesis, with a conversion of more than 99%. Y. lipolytica lipases can be good catalysts for ester hydrolysis reactions, even for ester synthesis, but are not good catalysts specifically for phytosterol esters synthesis.