This work aimed to formulate and perform physicochemical and functional characterization of maltodextrin microcapsules containing ethanolic extract of stevia, rich in antioxidant compounds, encapsulated by a spray-drying process with two maltodextrins (DE10 and DE19). The powders were named M10 and M19, respectively. We analyzed the physicochemical parameters, antidiabetic activity, cytotoxicity, bioaccessibility of the compounds by in vitro digestion, as well as the structure of the microcapsules by scanning electron microscopy. Microcapsules showed higher solubility (∼35%), lower moisture content (∼29%), and the maltodextrin DE10 had higher efficiency as an encapsulating agent (87%) when compared to DE19 (76%) and showed well-defined spherical structures. The microencapsulation preserved the content of phenolic compounds and antioxidant activity present in the extract (7.2% and 87.5%, respectively). The bioaccessibility of these microencapsulated compounds and antioxidant activity were higher under different conditions of in vitro digestion (mouth, gastric, and intestinal conditions) and showed no cytotoxic effects. We identified 41 compounds (by UHPLC-MS/MS-Qtof) related to the nutritional benefits offered by stevia and the microencapsulation technique can be recommended to preserve bioactive compounds.