PURPOSE: To effectively separate a water-soluble enzyme, when cells which contain the enzyme are ground, from cell fragments and other water-insoluble matter by contacting an aqueous medium which contains the water-soluble enzyme with clay, separating off the medium, and treating the medium.

CONSTITUTION: This separation of a water-soluble enzyme comprises keeping an aqueous medium in which a water-soluble enzyme is dissolved in contact with clay (preferably smectite or bentonite) in condition swelled with water and preferably in a quantity of 0.1-2 pts.wt. based on 10 pts.wt. of the aqueous medium, and subjecting the aqueous medium to a treatment for removing insoluble matter and/or non-enzymatic proteins from the aqueous medium (for example, centrifugal separation).