Mangosteen (Garcinia mangostana Linn.) is a functional fruit rich in highly beneficial metabolites, particularly xanthones, which exhibit various bioactive properties, including antioxidant and anti-inflammatory activities. Given its pharmaceutical benefits, the market demand for mangosteen is continuing to increase; however, little is known about the metabolic changes that occur during ripening. Here we used a combination of gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-MS (LC-MS) to simultaneously analyze the composition of primary and secondary metabolites in mangosteen fruit pericarp, aril, and seed at four different ripening stages (stages 0, 2, 4, and 6). A total of 57 and 98 metabolites were identified from GC-MS and LC-MS analyses, respectively. These metabolites comprised various metabolite classes, including sugars and derivatives, amino acids and derivatives, organic acids, an alcohol, aldehydes, glycosides, fatty acids, phenolics, alkaloids, terpenoids, xanthones, and a quinone. Our results showed that metabolites with variable influence on projection (VIP) >= 1.00 and p <= 0.05 included primary metabolites (e.g., L-mannopyranose, myo-inositol, arabinofuranose, galacturonic acid, L-(+)-tartaric acid and aspartic acid) and secondary metabolites (e.g., neoisostegane, epirobinetinidol-(4 beta,8)-catechin, alpha-mangostin, and gartanin). Such metabolites may contribute to the degradation of the cell wall, development of flavor, color, and aroma, and defense against frugivores, insects, and pathogens during mangosteen ripening. The metabolic pathways of galactose, ascorbate, aldarate, starch, sucrose, cysteine, and methionine, as well as glycolysis and the tricarboxylic acid (TCA) cycle, were differentially regulated during mangosteen ripening. Profiling the fruit metabolome during the ripening provided a snapshot for understanding the intricate biological and molecular regulation of fruit development. Our results will facilitate further improvements in post-harvest technologies that will help increase the shelf life of mangosteen fruit, thus assisting farmers and producers in the global commercialization of this superfruit.