Isolation and Purification - Isolation and purification is done immediately after termination of fermentation in a manner that retains the enzyme activity. If the cells are to be used for immobilization, the biomass is isolated and treated to make it ready for use.

The extracellular enzymes are recovered directly from broth, while enzymes localized within cells are isolated by rupturing the cells. Enzyme purification is based on various techniques whose efficacy and cost differ widely; the process used will mainly depend on the purity needed and the cost, which is acceptable.