Mangosteen (Garcinia mangostana Linn.) is a highly beneficial fruit, containing potent bioactive compounds such as xanthones. However, the metabolite comparisons of mangosteen pericarp, aril and seed have not been described in detail previously. A comparative approach was undertaken in the present work to evaluate the effects of different ratios of solvent combination in the metabolite extraction of mangosteen. Gas chromatography-based metabolomics approach was performed to evaluate the efficiency of two metabolite extraction methods utilising different solvent extraction ratios (3/1/1 v/v or 2/1/2 v/v of methanol/chloroform/water) in determining the primary metabolite composition of mangosteen fruit tissues (pericarp, aril and seed). Cumulatively, 43 known metabolites were putatively identified from the mangosteen fruit tissues. Due to the higher ratio of polar solvent (methanol and water) used in method 2 as compared to method 1, the former method preferentially extracted a higher number of polar metabolites. Conversely, the higher ratio of methanol solvent in method 1 also contributed to the identification of more alcohol metabolites. Additionally, the multivariate analysis revealed that mangosteen pericarp was mainly localised by ribonic acid, arabinopyranose, β-hydroxypyruvic acid, L-(+)-tartaric acid and galacturonic acid. Meanwhile, thymol-α-D- glucopyranoside and D-ribofuranose contributed to the separation of mangosteen aril, whereas mangosteen seed contained high levels of β-D-galactofuranose, L-threonic acid, butanoic acid, glycoside, malic acid and myo-inositol. Results suggested that the differing solvent ratios can highly influence the types and levels of the extracted metabolites. This finding highlights the influence of metabolite solvent extraction methods towards the end results of the extraction as well as the localisation of primary metabolites in different mangosteen fruit tissues. Hence, the present work is vital in revealing important spatial information of various metabolites toward a better understanding of the mangosteen fruit ripening process.