Honey is one of the most renowned natural foods. Its composition is extremely variable, depending on its botanical and geographical origins, and the abundant presence of functional compounds has contributed to the increased worldwide interest is this foodstuff. In particular, great attention has been paid by the scientific community towards classes of compounds like phenolic compounds, due to their capability to act as markers of unifloral honey origin. In this contribution the most recent progress in the assessment of new analytical procedures aimed at the definition of the qualitative and quantitative profile of phenolic compounds of honey have been highlighted. A special emphasis has been placed on the innovative aspects concerning the extraction procedures, along with the most recent strategies proposed for the analysis of phenolic compounds. Moreover, the centrality of validation procedures has been claimed and extensively discussed in order to ensure the fitness-for-purpose of the proposed analytical methods. In addition, the exploitation of the phenolic profile as a tool for the classification of the botanical and geographical origin has been described, pointing out the usefulness of chemometrics in the interpretation of data sets originating from the analysis of polyphenols. Finally, recent results in concerning the evaluation of the antioxidant properties of unifloral honeys and the development of new analytical approaches aimed at measuring this parameter have been reviewed.