The pulp and pericarp of mangosteen (Garcinia mangostana) fruit are popular food, beverage and health products whereby 60% of the fruit consist of the pericarp. The major metabolite in the previously neglected or less economically significant part of the fruit, the pericarp, is the prenylated xanthone alpha-mangostin. This highly bioactive secondary metabolite is typically isolated using solvent extraction methods that involve large volumes of halogenated solvents either via direct or indirect extraction. In this study, we compared the quantities of alpha-mangostin extracted using three different extraction methods based on the environmentally friendly solvents methanol and ethyl acetate. The three solvent extractions methods used were direct extractions from methanol (DM) and ethyl acetate (DEA) as well as indirect extraction of ethyl acetate obtained via solvent partitioning from an initial methanol extract (IEA). Our results showed that direct extraction afforded similar and higher quantities of alpha-mangostin than indirect extraction (DM: 318 mg; DEA: 305 mg; IEA: 209 mg per 5 g total dried pericarp). Therefore, we suggest that the commonly used method of indirect solvent extraction using halogenated solvents for the isolation of alpha-mangostin is replaced by single solvent direct extraction using the environmentally friendly solvents methanol or ethyl acetate.