Puerarin, also known as daidzein 8-C-glucoside, is a major isoflavone glycoside from Pueraria lobata. Puerarin has been shown to possess a variety of pharmacological activities. It has been widely used for the treatment of cardiovascular and cerebrovascular diseases. However, the further applications are limited due to its low water solubility and poor bioavailability. Structural modification is thus regarded as an efficient approach to improve the solubility and bioavailability of puerarin. Unlike chemical modifications, enzyme-assisted modifications, namely biocatalysis, is a promising alternative for the regioselective synthesis of puerarin derivatives due to its high selectivity. Up to date, acylation, glycosylation and hydroxylation of puerarin had been achieved through enzyme-based biocatalysis. Diverse active puerarin derivatives with improved solubility and bioavailability have been thus developed. Based on modification groups, this paper focused on the progress in the preparation of puerarin derivatives by biocatalysis, in which the whole-cells or pure enzymes were used as the biocatalysts. This article was expected to provide new ideas for the synthesis and development of puerarin drugs.