Species belonging to the Bauhinia genus, usually known as “pata-de-vaca”, are popularly used to treat diabetes. Bauhinia ungulata var. obtusifolia (Ducke) Vaz is among them, of which the leaves are used as a tea for medicinal purposes in the Amazon region. A microencapsulation study of lyophilized aqueous extract from Bauhinia ungulata leaves, which contain phenolic compounds, using five different wall materials (maltodextrin DE 4-7, maltodextrin DE 11-14; β-cyclodextrin; pectin and sodium carboxymethylcellulose) is described in this paper. The microstructure, particle size distribution, thermal behavior, yield, and encapsulation efficiency were investigated and compared using different techniques. Using high-performance liquid chromatography, phenolics, and flavonoids were detected and quantified in the microparticles. The microparticles obtained with a yield and phenolics encapsulation efficiency ranging within 60–83% and 35–57%, respectively, showed a particle size distribution between 1.15 and 5.54 µm, spherical morphology, and a wrinkled surface. Among them, those prepared with sodium carboxymethylcellulose or pectin proved to be the most thermally stable. They had the highest flavonoid content (23.07 and 21.73 mg RUTE/g Extract) and total antioxidant activity by both the DPPH (376.55 and 367.86 µM TEq/g Extract) and ABTS (1085.72 and 1062.32 µM TEq/g Extract) assays. The chromatographic analyses allowed for quantification of the following substances retained by the microparticles, chlorogenic acid (1.74–1.98 mg/g Extract), p-coumaric acid (0.06–0.08 mg/g Extract), rutin (11.2–12.9 mg/g Extract), and isoquercitrin (0.49–0.53 mg/g Extract), compounds which considered to responsible for the antidiabetic property attributed to the species.