The yerba mate (Ilex paraguariensis A.St.-Hil.) is abundant on phenolic compounds and their preservation by encapsulation can promote increased stability. The objective was to produce mate extract with a high concentration of bioactive compounds, microencapsulate and characterize them. A commercial yerba mate was used to produce the extracts and select the best extraction solvent (ethanol, water, and ethanol:water (1:1). The ethanol:water extract was encapsulated at 1:1 (w/w) by fructooligosaccharide (FOS) and gum arabic (GA), in different combinations: FOS, GA:FOS (1:3), GA:FOS (1:1), GA:FOS (3:1) and GA. The encapsulation of chlorogenic acids was around 80%, considering the major phenolic compounds by HPLC. Thermal stability, by DSC, increased at treatments FOS, GA:FOS (1:3), and GA:FOS (1:1) compare to the unencapsulated extract, and changes were noticed in ATR-FTIR bands and antioxidant activity. The encapsulated phenolic compounds from I. paraguariensis can be stable in food under heat processing.