BACKGROUND: Consumption of Spirulina-based functionalized food is usually unpleasant due to its specific sensorial properties. Therefore, Spirulina was encapsulated using alginate and whey protein concentrate (WPC) by emulsification method, and the effect of adding free and microencapsulated Spirulina (MS) to non-fat stirred yogurt was investigated during storage. RESULTS: Scanning electron microscope investigated microcapsules morphology and their mean particle size that was 52 ∼m, and electrostatic interaction between wall materials was illustrated by Fourier-transform infrared spectroscopy. The microspheres had appropriate encapsulation efficiency (44.54 ± 0.06%). Complete release of Spirulina from the microcapsules was observed in simulated intestinal fluid, which is favorable for Lactobacillus growth in human intestinal tract. Encapsulation caused meaningful differences in colorimetric factors, markedly in L*. Moreover, free and MS were added to yogurt samples, and the results showed that the physicochemical properties (pH, color, viscosity, water holding capacity and susceptibility to syneresis) and sensorial assessment of MS yogurt were positively affected. During the storage, MS yogurt had higher pH value than the others; furthermore, it showed the lowest syneresis and a constant increase in viscosity. Finally, the sensory evaluation results of MS yogurt, in comparison with the free form of Spirulina utilization, indicated improved acceptance of the produced functional food. CONCLUSION: Results showed an obvious impact of encapsulation on the physicochemical properties of yogurt containing MS. The sensory evaluation showed that encapsulation could generally enhance the customer's satisfaction. It can be stated that masking microalgae color and flavor by microencapsulation could be used for dairy products fortification by microalgae.