The aim of the present work was to control phytopathogens associated to mango decay by exposure to antifungal thyme oil-starch/agave fructans microcapsules in Nylon sachets. Fusarium pseudocircinatum, Alternaria alternata, Neofusicocum kwambonambiense, Cladosporium pseudocladosporioides, and Colletotrichum gloeosporioides were isolated from mango fruits and its mycelial growth was 100% inhibited with 5 μL of thyme oil. Thyme oil was microencapsulated with modified starch/agave fructans by spray drying. Thymol content, size, and shape of microcapsules were evaluated. Antifungal sachets were prepared by filling Nylon bags (4 × 4 cm) with different doses of thyme oil microcapsules: 0.10, 0.15 and 0.20 g. The mycelial growth of all microorganisms was controlled with 0.10, 0.15 and 0.20 g of antifungal sachets. The incidence (75 and 65%) and severity (77 and 41%) of C. gloeosporioides were effectively reduced in mango, respectively, using 0.10 and 0.20 g of antifungal sachets.