Food waste is a global concern with enormous economic, environmental and social impacts that has contributed to active packaging evolution. However, incorporating bioactive substances into the packaging can deteriorate its physicochemical and mechanical characteristics. Thus, the objective of this work was to entrap the natural bioactive compound thymol into microparticles and apply them in the form of pads for the controlled release of bioactivity in food packaging material. The physicochemical characteristics and bioactivity of five different ethyl cellulose-based microparticles were evaluated. Increasing the amount of thymol in the formulation led to higher encapsulation efficiency. Encapsulation resulted in a substantial increase of >10–20 °C in the volatilization temperature of thymol, and the release of thymol occurred following a sustained profile, best described by the Higuchi release kinetic model. Increasing the polymer to thymol ratio in the microparticles resulted in higher thermal stability and a more gradual release profile. While all formulations demonstrated considerable inhibition of E. coli growth, the ones with the highest thymol content maintained their antimicrobial activity for at least one month of microparticle storage. Furthermore, the ability of the microparticles in retaining pH and titratable acidity of cherry tomatoes was evaluated, and it was confirmed that these characteristics were maintained during 21 days of storage.