Food-derived bioactive peptides (FBPs), a class of short-chain amino acid peptides produced by the hydrolysis of natural food proteins, have a variety of excellent functional activities and may play an important role in promoting human health and preventing the development of chronic diseases. However, FBPs generally suffer from bitter taste, high hygroscopicity, poor stability and low bioavailability, which restricts their application in food and medicine fields. A delivery system is commonly used for the encapsulation, protection and delivery of bioactive components. Therefore, choosing a suitable delivery system for FBPs is important for improving the stability and bioavailability of FBPs. This article reviews the major challenges facing the application of FBPs in the food industry, with a focus on the types, characteristics, advantages and disadvantages of FBP delivery systems, and discusses the current problems and future research directions of FBP delivery systems, in order to provide new ideas and guidance for the design, preparation and research of FBP delivery systems.