The phytochemical investigation of the MeOH extract of Garcinia mangostana (mangosteen, Clusiaceae) pericarps affords a new xanthone namely, garcixanthone D (1,3,5,6,7‐pentahydroxy‐2,8‐bis(3‐methylbut‐2‐enyl)‐xanthone) (5), and four known metabolites: β‐mangostin (1), α‐mangostin (2), rubraxanthone (3), and garcinone E (4). Their structures are assigned using high resolution mass spectrometry (HRMS), nuclear magnetic resonance (NMR), ultraviolet (UV), and infrared (IR) spectroscopic analyses, as well as through comparison with published data. The isolated metabolites are assessed for their α‐amylase inhibitory (AAI) potential. Compounds 4 and 5 have the highest activity, with a % inhibition of 93.8 and 85.6, respectively, compared to acarbose (96.4%, reference α‐amylase inhibitor). The molecular docking studies of the tested metabolites are expected to provide a rational explanation for the AAI activity results. Moreover, their pharmacokinetic parameters are assessed using Swiss ADME. It is noteworthy that compounds 4 and 5 have different binding poses compared to acarbose. They possess activity via different modes, such as H‐bonding, pi‐pi stacking, hydrophobic, and Van der Waal interactions. These data reinforce the health benefit of mangosteen as an alternative medicine to help to decrease postprandial glucose absorption. Therefore, mangosteen could have good potential for the treatment and/or prevention of diabetes and obesity.