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The temporal metabolomes associated with Rubus coreanus (RC) vinegar production were delineated using mass spectrometry-based metabolomic analyses with multivariate studies. We observed a clustered pattern of 27 discriminant metabolites: 4 organic acids, 9 sugars and sugar derivatives, 2 alcohol and carboxylic acid, 6 esters, and 6 terpenes. The levels of organic acids and alcohols were steadily decreased throughout fermentation, whereas those of sugars and sugar derivatives, carboxylic acids, esters, and terpenes peaked at 6 days. Further, the in vivo nutraceutical potentials of RC vinegar were examined with its metabolomic implications for bone health in growing rat model. Intriguingly, the plasmatic metabolomes among treated rat groups were observed with lower levels of non-essential amino acids and lysophosphatidylcholines (LysoPCs) coupled with higher levels of fatty acids and bile acids. The plasmatic metabolomes complemented with bone morphometric and clinical parameters suggest the bone health ameliorating effects of RC vinegar.