IntroductionThe genus Clusia L. is mostly recognised for the production of prenylated benzophenones and tocotrienol derivatives.ObjectivesThe objective of this study was to map metabolome variation within Clusia minor organs at different developmental stages.Material and MethodsIn total 15 organs/stages (leaf, flower, fruit, and seed) were analysed by UPLC‐MS and 1H‐ and heteronuclear multiple‐bond correlation (HMBC)‐NMR‐based metabolomics.ResultsThis work led to the assignment of 46 metabolites, belonging to organic acids(1), sugars(2) phenolic acids(1), flavonoids(3) prenylated xanthones(1) benzophenones(4) and tocotrienols(2). Multivariate data analyses explained the variability and classification of samples, highlighting chemical markers that discriminate each organ/stage. Leaves were found to be rich in 5‐hydroxy‐8‐methyltocotrienol (8.5 μg/mg f.w.), while flowers were abundant in the polyprenylated benzophenone nemorosone with maximum level detected in the fully mature flower bud (43 μg/mg f.w.). Nemorosone and 5‐hydroxy tocotrienoloic acid were isolated from FL6 for full structural characterisation. This is the first report of the NMR assignments of 5‐hydroxy tocotrienoloic acid, and its maximum level was detected in the mature fruit at 50 μg/mg f.w. Seeds as typical storage organ were rich in sugars and omega‐6 fatty acids.ConclusionTo the best of our knowledge, this is the first report on a comparative 1D‐/2D‐NMR approach to assess compositional differences in ontogeny studies compared with LC‐MS exemplified by Clusia organs. Results derived from this study provide better understanding of the stages at which maximal production of natural compounds occur and elucidate in which developmental stages the enzymes responsible for the production of such metabolites are preferentially expressed.