Limonene is a monoterpene flavor compound found in several beverages. However, it easily degrades by oxidation reactions at acidic environment contributing to an undesirable off-flavor. Encapsulation technologies can protect compounds from degradation. This work focuses on the effect of using complexes of limonene with α-, β-, and γ- and HP-β-cyclodextrins in non-alcoholic beverages to improve flavor and shelf-life stability due to the chemical structure of cyclodextrins. Spray-drying technology was applied to prepare different cyclodextrin/limonene forms, from which the most promising was selected and further applied in simulated lemon juice beverages. Different drying process conditions were tested, namely feed temperature (120, 160, and 180 °C) and setting of prior incubation (temperature, room and 50 °C; time, 0.17 and 24 h). An inlet temperature of 160 °C favored the encapsulation of limonene into resulting nano/microparticles. Moreover, incubation for 24 h enhanced limonene retention for all complexes, especially for β-cyclodextrin/limonene complexes, which achieved 66% of encapsulation efficiency and a 6.25 w/w of limonene load. The β-cyclodextrin/limonene particles which enabled higher load (160 °C, 24 h) presented particle size ranging between 1 and 3 μm and were chosen to undergo an accelerated aging process in a lemon juice beverage model. This study revealed that the limonene content decreased over time for model and supplemented juice, but decreased less when β-cyclodextrin/limonene particles were added. After 10 days, which mimics 9 months of storage, 40% of complexed limonene remained in the model beverage.