Microstructure is closely related to techno-functional properties in microencapsulated powders intended to protect bioactive compounds. Soursop leaves provide phytochemicals that need to be protected to ensure their functionality. This investigation aimed to study the microstructure of microcapsules containing soursop leaves extract and its linkage with physical and chemical characteristics of the resulting powder. Microcapsules were prepared by spray drying using gum Arabic and maltodextrin as encapsulating agents at 5 and 10%. Powders were characterized by scanning electron microscopy, particle size analysis, solubility, infrared spectroscopy and encapsulation efficiency. Microphotographs showed spherical shape particles ranging from 0.25 to 13.87 μm, where the particles morphology depended on the concentration and the type of the encapsulant used. At higher concentration of encapsulant, there was an increase in the sphericity, integrity, size, and surface smoothness of particles. This relationship was inverse for solubility in treatments with gum Arabic. The extract encapsulation was confirmed by Fourier Transform infrared spectroscopy and encapsulation efficiency index, revealing that the treatment with maltodextrin at 10% showed a better capability for entrapment (72.12%). The results evidence that microstructure of microcapsules is closely linked to the type and concentration of encapsulant, which in turn determine the physical and chemical characteristics of powders intended for instant drinks solubility and entrapping soursop bioactive compounds.