Transglutaminase (TG) is an alternative coacervate cross-linking agent to aldehydes due to its safety. In this work, the cross-linking conditions of soybean protein isolate (SPI)-chitosan coacervates with TG-utilizing capsanthin as the model core were optimized and its cross-linking effectiveness was compared with that of glutaraldehyde. Results indicated that the optimum capsanthin microcapsule cross-linking conditions were as follows: a suspension pH of 6.0, an incubation duration of 3 h, a TG concentration of 18.75 U/g SPI and a reaction temperature of 45 degrees C. Under these conditions, TG provided a cross-linking effectiveness comparable with that of glutaraldehyde in regards to microcapsule stability against swelling in 80 degrees C water and heating at 150 degrees C. Differential scanning calorimetry analysis revealed that TG cross-linking increased the integrity of the microcapsule walls. It was concluded that the SPI-chitosan coacervation pair has potential applications in the food industry in terms of cross-linker safety and effectiveness.