The phase separation kinetics of an ethanolic L-menthol solution in an aqueous solution of optically and biologically active chitosan L-and D-aspartate was studied. It has been established that this process proceeds according to the extraction crystallization mechanism and combines two types of phase separation, namely: liquid-liquid and liquid-crystal. The effect of aspartic acid stereoisomer, chitosan molecular weight, and polymer: acid ratio on the optical, structural-morphological, and dimensional characteristics of dispersed phase droplets at the initial stage of phase separation and crystal aggregates of the L-menthol condensed phase at the final stage was assessed. In the chitosan D-aspartate medium, as well as with an increase in the concentration of components in the optically active medium and the molecular weight of the polymer, the rate of phase separation, the size of droplets and particles increase. It has been suggested that the system under study is promising for encapsulating hydrophobic drugs, creating chirooptic waveguides, and sensors for biomedical purposes, as well as developing new methods for studying the fundamental principles of phase separation in intracellular regulation of membraneless organelles and subcellular organization of biosystems, including under stress conditions of a living organism underlying the development of new pharmaceuticals to treat rare and currently incurable diseases.