In this study, the microencapsulation of Swiss cheese bioaroma through spray drying was examined. The fermented whey permeate (bioaroma) produced by Propionibacterium freudenreichii was characterized and used as active for microencapsulation process using spray drying. The effect of inlet air temperature drying (Ti), and modified starch concentrations (% MS) was evaluated using the response surface methodology to examine the physical, chemical and morphological properties of various microparticles produced. The rheological analysis of suspensions prepared with different concentrations of modified starch in maltodextrin combination showed that Newtonian model was appropriate to describe the characteristics of flow. It was found that greater retention of acetic and propionic acids was obtained with intermediate air inlet temperature and modified starch concentrations (175°C; 50% MS), and the extreme values of the variables resulted low retentions. Lower values of moisture and water activity were obtained with 50% of modified starch, and the temperature influenced positively only in water activity of the microparticles. The bulk density and average particle diameter were positively influenced by the concentration of modified starch, and interaction of air inlet temperature and starch concentration only influenced the average diameter of the microparticles. The morphology of the particles had a spherical shape with diameters varying between microns and millimeters.