The aim of this research was to develop an enzyme encapsulation process in which both the complex coacervation and drying processes are combined into a single step. For this purpose, we used a novel three-fluid nozzle at the atomization step of spray drying. -Amylase as a model enzyme was encapsulated by coacervation in calcium (Ca) alginate and Ca-alginate+chitosan shell matrices and the powder was obtained in a single step through spray drying. The single-step process was compared to carrying out the complex coacervation and drying processes in two steps using freeze drying, in which -amylase was encapsulated by carrying out the complexation process in the above-mentioned shell matrices using the same three-fluid atomizer and collecting the coacervates, which were subsequently freeze dried. The results showed that the microcapsules obtained from the single-step encapsulation process (three-fluid nozzle spray drying) had smaller particle sizes, were less porous, and provided better enzyme stability compared to the microcapsules obtained by carrying out the complexation and drying in two steps and the single-step process was faster. It was observed that the egg-box structure was formed in both types of powder particles; however, the complexation with chitosan partially disrupted the formation of this structure. The three-fluid nozzle-based spray drying is a promising technology in which both the complex coacervation and drying processes can be carried out in a single step.