Buriti and pequi oils are rich in carotenoids and beneficial to human health; however, carotenoid oxidation during storage causes color loss in foods, making it difficult to use these oils in food products. This research aimed to encapsulate pequi oil and co-encapsulate pequi and buriti oils by emulsification using whey protein isolate (WPI) as an emulsifier in two forms, natural (unheated) and heated, followed by freeze-drying. The emulsions were studied by droplet size under different stress conditions, instability index, and rheology. The freeze-dried (FD) samples were studied after accelerated oxidation and the total carotenoid retention was determined; for the reconstituted FD, the zeta potential and droplet size were recorded after storage at 37°C for 30days. The emulsions were stable in all conditions, with average droplet sizes between 0.88±0.03 and 2.33±0.02μm, and formulations with heated WPI presented the lowest instability index values. The FD's zeta potential values ranged from -50±3 to -32±3mV. The co-encapsulated oils presented higher carotenoid retention (50±1 and 48±1%) than the free oils (31±2%) after 30days. The oxidative stability indexes were 51±4 and 46±3 for the co-encapsulated oils with unheated and heated WPI, respectively, and 20.5±0.1h for the free oils. FD formulations with 1:3 ratio of oil: aqueous phase and heated or unheated WPI showed the best carotenoid retention and oxidative stability, indicating that FD oil emulsions have potential as next-generation bioactive compound carriers.