Biocatalysis is one of the greenest technologies for the synthesis of chiral molecules due to exquisite regioselectivity and stereoselectivity in water under mild conditions. For example, protection and deprotection of functional groups are usually not required for biotransformations, high or low temperature reactions can often be circumvented and usage of organic solvents are drastically minimized. To truly empower the green chemistry feature of biocatalysis, it is essential to integrate enzymatic transformations strategically into chemical transformations at the retrosynthetic level. This review focuses on the development of novel biocatalytic pharmaceutical processes to replace chemical routes with poorer process efficiency and higher manufacturing costs.