Phycocyanin is a source of natural blue dye which can be extracted from Spirulina sp. The main characteristics of phycocyanin are unstable by temperature and pH during processing and storage. Microencapsulation methods could be proposed to protect the phycocyanin from the external effect, where the types and concentration of encapsulant used may affect the characteristics of the result. The aim of this study was to determine the best formulation and characterization of phycocyanin microcapsules from Spirulina sp. with maltodextrin and alginate as an encapsulant. The microcapsules were produced using five different concentrations of alginate in maltodextrin, namely 0%; 0.2%; 0.4%; 0.6%; and 0.8% (w/w). The total encapsulant used was 10% of phycocyanin microparticle solution. The results showed that the increasing concentration of alginate could raise the levels of phycocyanin, moisture content, encapsulation efficiency, bulk density, blue intensity, and particle size, it also improved the morphology of the microcapsules. Phycocyanin microcapsules with alginate concentration of 0.6% and 9.4% maltodextrin had the highest phycocyanin content, encapsulation efficiency, and blue intensity.