The purpose of this work was to replace modified starch (SF) by inulin (IN), a prebiotic carbohydrate, during emulsification assisted by ultrasound. Oregano extract was encapsulated using five proportions of IN and SF as wall materials. The effect of such substitution on the microparticle characteristics was evaluated. Attempting to contribute with the increasing demand for prebiotic consumption, mixing one part of SF with three parts of IN (1:3, mass basis) yielded encapsulation efficiency equal to 66±1% and the largest thymol retention: 84±9%. Besides the entrapment of thymol, high amount of other compounds present in oregano extract could be entrapped in the polymeric matrix: 92±1%. Reduction of the microparticles sizes when increasing the proportion of inulin was also observed. Comprising such results and those presented for powder morphology, surface extract, particle size distribution, X-ray diffraction and thermal stability, the proportion 1:3 (SF:3IN) is a favorable prebiotic encapsulant matrix for encapsulating oregano extract and retaining target bioactive compounds.