Acerola (Malpighia emarginata DC.) is a sub-tropical and tropical fruit renowned for its high levels of vitamin C and phenolic compounds, which offer health benefits. This study aimed to optimize the spray drying process by determining the inlet and outlet temperatures using response surface methodology (RSM) with the central composite design. Additionally, it aimed to evaluate the release kinetics in the hydrophilic food simulation environment and the stability of the resulting powder under various storage temperatures. The RSM method determined the optimal inlet and outlet temperatures as 157 °C and 91 °C, respectively. High-accuracy prediction equations (R2 ≥ 0.88) were developed for moisture content (3.02%), process yield (91.15%), and the encapsulation yield of total polyphenol content (61.44%), total flavonoid content (37.42%), and vitamin C (27.19%), with a predicted monolayer moisture content below 4.01%, according to the BET equation. The powder exhibited good dissolution characteristics in the acidic hydrophilic food simulation environment and showed greater stability when stored at 10 °C for 30 days, compared to storage at 35 °C and 45 °C.