Fluorescence imaging has emerged as a promising technique for monitoring and assessing various biologically relevant species in cells and organisms, driving the demand for effective fluorescent agents with good biocompatibility and high fluorescence performance. However, traditional fluorescent agents, such as quantum dots (QDs) and organic dyes, either suffer from toxicity concerns or poor fluorescence performance (e.g., low photobleaching-resistance). In this regard, citrate-based fluorescent biomaterials, which are synthesized from the natural and biocompatible precursor of citric acid (CA), have become competitive alternatives for fluorescence imaging owing to their biocompatibility, cost effectiveness, straightforward synthetic routes, flexible designability, as well as strong fluorescence with adjustable excitation/emission wavelengths. Accordingly, numerous citrate-based biomaterials, including carbon dots (CDs), biodegradable photoluminescent polymers (BPLPs), and small molecular fluorophores, have been developed and researched in the past few decades. This review discusses recent progress in the research and development of citrate-based fluorescent materials with emphasis on their design and synthesis considerations, material properties, fluorescence properties and mechanisms, as well as biomedical applications. It is expected that this review will provide an insightful discussion on the citrate-based fluorescent biomaterials, and lead to innovations for the next generation of fluorescent biomaterials and fluorescence-based biomedical technology.