The interaction between whey proteins and carotenoid is reported to improve carotenoid solubility and stability, however, the strong trend of carotenoids to aggregate when in polar systems is often neglected in papers addressing their molecular interaction. Therefore, this study focused on characterizing the aggregative behavior of the carotenoids from yellow mombin (Spondias mombin) and to understand how these carotenoids behave when added to aqueous dispersions of whey proteins. Carotenoids-rich extract, containing mainly β-cryptoxanthin and lutein, was obtained from freeze-dried yellow mombin pulp and its aggregative behavior in ethanol/water medium was studied. By increasing the medium polarity, carotenoids trend to form J-aggregation, causing a drop in the color intensity of the solution. When added to whey protein aqueous dispersions, rather than a protein-carotenoid bimolecular interaction, the formation of co-aggregates between carotenoids and whey proteins was evidenced by preparative size exclusion chromatography. These results may contribute to the developing functional food products.