Coffee (Coffea arabica L.) is one of the most consumed non-alcoholic beverages. To expand the coffee market and attract consumers to a diversity of coffee types, data on the nutritional potential of different coffee varieties are needed. The present study assessed the phytochemical constituents, i.e., total flavonoid content (TFC), total anthocyanin content (TAC), and total phenolic content (TPC), and the antioxidant activities of extracts from Bourbon coffee berries differing in color. Furthermore, the metabolome profiles of the four Bourbon berries, i.e., purple (PF), red (RF), orange (ORF), and yellow (YF), were explored. The results indicated that the TFC and TPC were significantly higher in RF (7.12 ± 0.96 and 9.01 ± 1.36 mg/g), followed by YF (6.54 ± 0.38 and 7.80 ± 0.10 mg/g), ORF (6.31 ± 0.15 and 7.20 ± 0.40 mg/g), and PF (4.66 ± 0.53 and 6.60 ± 1.10 mg/g). A UPLC-MS/MS analysis resulted in the identification of 579 metabolites belonging to 11 different compound classes. Of these, 317 metabolites were differentially accumulated in the four varieties. These differentially accumulated metabolites were majorly classified as flavonoids, organic acids, phenolics, and amino acids and derivatives. Based on the metabolome profiles, we discuss the major compounds in each Bourbon coffee variety and highlight their nutritional and health potentials. These findings will serve as a foundation for the promotion of each variety and provide useful information for coffee improvement programs.