Abstract Phycocyanin as antioxidants is a special pigment in Spirulina platensis that belongs to the temperature-sensitive. Microencapsulation of S. platensis is needed to maintain the phycocyanin content. The aimed of this study was to determine the effect of microencapsulation and different temperatures (40 °C and 100 °C) process to phycocyanin degradation, the relative concentration (CR) of phycocyanin, the antioxidant degradation and total color different (TCD) and its interaction. The result shown the microencapsulation process could increase the stability of phycocyanin against temperature. The higher heating processes cause an increase in phycocyanin degradation. The interaction between high temperature treatment and microencapsulation produced the highest value of phycocyanin degradation (57.23±0.16%) and antioxidant degradation (46.85±0.04%), namely S. platensis powder (without microencapsulation) with a temperature of 100 °C, while the highest of phycocyanin CR (95.72±0.13%) at S. platensis microcapsules with a temperature of 40 °C. However, microencapsulation gave a higher TCD value of S. platensis caused by the Maillard reaction.