Mauritia flexuosa L.f. is a palm tree which presents great morphological variability (morphotypes), represented mainly by the mesocarp color of its fruits. The objective of the study was to characterize the physicochemical and antioxidant properties of three morphotypes of Mauritia flexuosa L.f. (“Yellow”, “Colour” and “Shambo”) of greater economic importance in the Peruvian Amazon. “Shambo” showed a significantly high content of bioactive compounds (total phenolics, flavonoids and carotenoids) and DPPH radical scavenging activity compared to the “Yellow” and “Colour” morphotypes (p ≤ 0.05). There was a significant correlation between DPPH radical scavenging activity and total phenolics, flavonoids and carotenoids (p ≤ 0.01). Furthermore, milk-based beverages enriched with carotenoids of those morphotypes of Mauritia flexuosa L.f. have been shown to be a good source of bioactive compounds for use in the food industry. The milk-based beverages enriched with carotenoids of those morphotypes of Mauritia flexuosa L.f. showed higher lightness (L∗) and yellowness (b∗).