Abstract: This study examined the changes in flavonoid and carotenoid metabolites in the peel of Coffea arabica L. in mature and immature stages and their roles in coloration. Ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) was employed to analyze the metabolite profiles, in combination with principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA), and clustering analysis. A total of 234 flavonoid metabolites and 40 carotenoid metabolites were detected, with flavonols (81 species) and lutein (34 species) being the most abundant. The total carotenoid content in the peel decreased significantly after ripening, while the total flavonoid content remained relatively stable, although anthocyanin accumulation showed the opposite pattern. Lutein and β-carotene accumulation in unripe peels were linked to green coloration, while cyanidin derivatives contributed to red coloration in ripe peels. Furthermore, unique accumulations of phytoene and phytofluene were observed in the ripe peels. This study elucidates the relationship between flavonoid and carotenoid accumulation and peel coloration during the ripening of Coffea arabica L. and provides new insights into the mechanisms underlying coffee peel coloration, offering a theoretical foundation for the utilization of coffee by-products and the development of functional foods.