This study examined the effect of microencapsulation on effective compounds of Angelica (Heracleum persicum) essential oil during storage. To this end, oil-in-water emulsions containing 10% Angelica (wall material basis) in an aqueous solution of 5 and 10% wall materials (β-cyclodextrin and sodium caseinate) were prepared by ultrasound (40% intensity for 3 min and a frequency of 200 kHz); then, the mixtures were dried by freeze-drying. The characteristics of the microcapsules, such as encapsulation efficiency (EE), moisture content, bulk density, particle size, scanning electron microscopy (SEM), phenolic compounds, and the Ferric Reducing Ability of Plasma (FRAP), were evaluated. During the 45 days of storage at varying temperatures (4 and 25˚C) and relative humidity (RH) (52.89±0.22%, 75.29±0.12%), the quick release of the active compounds was evaluated. The results indicated that microencapsulating with sodium caseinate provided better protection for the compounds compared to beta-cyclodextrin. Increasing the concentration of wall material from 5% to 10% led to higher amounts of active ingredients in the microcapsules. The microcapsules containing beta-cyclodextrin were spherical in shape and had numerous indentations, voids, and cracks. Meanwhile, the microcapsules containing sodium caseinate had thin and uniform walls without pores, appearing in the form of flakes. The microcapsules with 10% beta-cyclodextrin wall material had the highest bulk density at 593 kg/m3, while the microcapsules with 5% sodium caseinate wall material had the lowest bulk density at 49.67 kg/m³. The diameter range of the particles was consistent, with the 10% sodium caseinate microcapsules being slightly larger. Over the 45 days of storage, the number of active compounds decreased, with microcapsules containing 10% sodium caseinate showing the least reduction in phenolic compounds, which was considered the optimal treatment. The optimal microencapsulated powder can be used as a natural flavoring agent in food.