Extracellular lipase from Yarrowia lipolytica was immobilized by ionotropic gelation with alginate and chitosan as encapsulating agents. Photomicrographs revealed a collapsed and heterogeneous surface of these microcapsules due to freeze-drying process. The optimum reaction temperature for the microencapsulated lipase (40 °C) was higher than for free lipase (35 °C) as well as the optimum pH (8.0 and 7.5, respectively). The study of the reaction kinetics showed that a higher maximum reaction rate (V) (221.1 U/mg) for the free lipase in comparison to the immobilized form (175.3 U/mg). A protective effect of the microcapsule was detected in the storage of the enzyme at room temperature, as after 75 days 35% of activity was maintained for the microcapsules, while no activity remained after 15 days with the free enzyme. Lower values for inactivation constant (k) and increase in half-life for immobilized lipase showed that lipase microencapsulation favored the thermostability of this enzyme.