Microbial metabolites, the diverse array of small molecules produced by microorganisms that play a pivotal role in various biological processes, hold immense potential for advancements in medicine, biotechnology and environmental science. To harness this potential, comprehensive databases are essential for cataloguing, characterizing and analysing these compounds. This chapter provides a comprehensive overview of existing microbial metabolite databases, exploring their scope, structure and utility. Key databases such as Kyoto Encyclopedia of Genes and Genomes (KEGG), BioCyc, MetaCyc, MiMeDB, Human Metabolome Database (HMDB) and MPMdb are discussed, highlighting their critical role in connecting microbial diversity with metabolic function. By understanding the landscape of available databases, researchers can effectively explore the complex world of microbial metabolites and unlock their full potential. Additionally, we highlight the importance of data integration, quality and continuous updates in maximizing the value of these databases for advancing our knowledge of microbial metabolism and its implications for the environment.