To date, no study has investigated the variation of the primary metabolite profile of the fruit of Flacourtia indica (Burm.f.) Merr. (commonly known as governor’s plum), an underutilised fruit in Jamaica. To fill this gap, the current study aimed to bring novel data on this fruit at two different ripe stages (light = deep wine-red colour and dark = fully darkened brown colour) and explore the variation of their metabolome profiles. The gas chromatography-mass spectrometry (GC-MS) profiling identified 10 saccharides, 4 sugar alcohols, 11 organic acids, 24 fatty acids, and 8 amino acids in the light and dark colour fruits. However, some metabolites were not shared by both fruit ripening stages. The principal component analysis (PCA) of the different classes of the primary metabolites showed that the significant difference between the light and dark colour governor’s plum fruit is mainly determined by the content of sugars and organic acids, with the fully ripe (dark) stage expressing significant high levels of both. The hierarchical cluster analysis (HCA) showed that the profiled sugars, sugar alcohols, and fatty acids were grouped into two main clusters. In contrast, organic acids and amino acids were grouped into one cluster. However, some metabolites were related to the clusters observed. With these profiles, it was concluded that the dark colour governor’s plum is in the true ripe stage, although the light colour fruit is commercially considered ripe.

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