The metabolome of Rubus coreanus Miquel fruit (bokbunja) was characterized by simultaneously analyzing 92 samples to elucidate the integrative metabolic factors associated with 4 different regions and 3 levels of maturity. The region- and maturity-specific metabolomic differences were characterized using ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC–qTOF-MS). Unsupervised multivariate proved capable of classifying the metabolite profiles associated with the different regions and maturity levels. The maturity levels induced major clusters in which the most distinctive metabolic phenotypes were observed in the immature and middle-mature bokbunja cultivated in the Gok-sung region. The resultant loading score plot revealed that tannins, proanthocyanidins, and anthocyanidins were the metabolic features that differentiated the maturity levels. Furthermore, applying a multivariate extension of a univariate analysis of variance (ANOVA) isolated the region-dependent metabolic markers that are independent of the ripening stage (e.g., procyanidin dimer B4 and galloyl-HHDP-glucose). These metabolites are important bioactive compounds as well as determinants of taste quality. Our results could be useful in monitoring and producing black raspberry-related foods with superior functional, flavor, and medicinal qualities.