Metabolites have been developed for crystals with diverse morphologies and functionalities. These materials are self-assembled into various nanostructures, exhibiting excellent piezoelectric, semiconducting, optical, thermal, and mechanical properties. Due to the metabolites' excellent biocompatibility and biodegradability, the metabolite-based assemblies have found wide applications in wearable technologies, biomedical fields, and many other areas. In this paper, we review the synthesis methods and self-assembly mechanisms of metabolites and then discuss their versatile properties. We also highlight recent advances in energy harvesting, energy storage, and biomedical applications enabled by the metabolite self-assemblies and identify current challenges and potential directions of breakthroughs in studying metabolite assemblies.