Guaraná byproducts are rich in carotenoids, featuring strong antioxidant capacity and health-promoting benefits. However, these compounds are highly susceptible to oxidation and isomerization, which limits their applications in foods. This research aimed to encapsulate the carotenoid-rich extract from reddish guaraná peels by spray drying (SD), chilling (SC), and their combination (SDC) using gum arabic and vegetable fat as carriers. The carotenoid-rich extract was analyzed as a control, and the formulations were prepared with the following core–carrier ratios: SD20 (20:80), SD25 (25:75), SD33 (33:67), SC20 (20:80), SC30 (30:70), SC40 (40:60), SDC10 (10:90), and SDC20 (20:80). The physicochemical properties of the formed microparticles were characterized, and their storage stability was evaluated over 90 days. Water activity of microparticles formed during the SD process increased during storage, whereas those formed by SC and SDC processes showed no changes in water activity. The formed microparticles exhibited color variation and size increase over time. Carotenoid degradation of the microparticles was described by zero-order kinetics for most treatments. Considering the higher carotenoid content and its stability, the optimum formulation for each process was selected to further analysis. Scanning electron micrographs revealed the spherical shape and absence of cracks on the microparticle surface, as well as size heterogeneity. SD increased the stability to oxidation of the carotenoid-rich extract by at least 52-fold, SC by threefold, and SDC by 545-fold. Analysis of the thermophysical properties suggested that the carrier and the process of encapsulation influence the powder’s thermal resistance. Water sorption data of the SDC microparticles depended on the blend of the carrier agents used in the process. Carotenoid encapsulation via an innovative combination of spray drying and spray chilling processes offers technological benefits, which could be applied as a promising alternative to protect valuable bioactive compounds.