Sequential enzymatic cross-linking and heat pretreatments were used in this work to enhance the heat stability of whey protein isolate (WPI). In the first route, WPI was cross-linked by transglutaminase before incorporation in microemulsions for heat pretreatment at 90 degrees C for 20 min. In the second route, WPI was cross-linked by transglutaminase within microemulsions before thermal pretreatment. Particles produced from the two routes were different in dimension and heat stability and were also affected by the ratio of WPI and enzyme and cross-linking duration. At appropriate conditions, for example, 10 h of cross-linking by transglutaminase equivalent to 5% mass of WPI using the first route, a 5% dispersion (pH 6.8 and 100 mM NaCl) of the produced nanoparticles remained clear after heating at 90 degrees C for 20 min. In comparison, nanoparticles produced by thermal pretreatment only in a microemulsion corresponded to a translucent, flowable dispersion, whereas native WPI formed a gel. This novel approach can be used to manufacture heat-stable whey protein ingredients for clear beverage applications.