This review presents the latest research on chromatography-based metabolomics for bioorganic research of honey, considering targeted, suspect, and untargeted metabolomics involving metabolite profiling and metabolite fingerprinting. These approaches give an insight into the metabolic diversity of different honey varieties and reveal different classes of organic compounds in the metabolic profiles, among which, key metabolites such as biomarkers and bioactive compounds can be highlighted. Chromatography-based metabolomics strategies have significantly impacted different aspects of bioorganic research, including primary areas such as botanical origins, honey origin traceability, entomological origins, and honey maturity. Through the use of different tools for complex data analysis, these strategies contribute to the detection, assessment, and/or correlation of different honey parameters and attributes. Bioorganic research is mainly focused on phytochemicals and their transformation, but the chemical changes that can occur during the different stages of honey formation remain a challenge. Furthermore, the latest user- and environmentally friendly sample preparation methods and technologies as well as future perspectives and the role of chromatography-based metabolomic strategies in honey characterization are discussed. The objective of this review is to summarize the latest metabolomics strategies contributing to bioorganic research onf honey, with emphasis on the (i) metabolite analysis by gas and liquid chromatography techniques; (ii) key metabolites in the obtained metabolic profiles; (iii) formation and accumulation of biogenic volatile and non-volatile markers; (iv) sample preparation procedures; (v) data analysis, including software and databases; and (vi) conclusions and future perspectives. For the present review, the literature search strategy was based on the PRISMA guidelines and focused on studies published between 2019 and 2024. This review outlines the importance of metabolomics strategies for potential innovations in characterizing honey and unlocking its full bioorganic potential.
