Particle-stabilized emulsions have shown increasing potential application in food emulsion systems. Here, soy protein, an abundant and inexpensive plant-based protein, was used to develop nanoparticles for emulsion stabilizer applications. An enzymatic cross-linking method based on microbial transglutaminase (mTG) was developed for the fabrication of soy protein nanoparticles (SPNPs). The emulsion stability was compared between soy protein isolate (SPI) and three different nanoparticles. The size of SPNPs ranged from 10 nm to 40 nm, depending on the production conditions. The emulsions stabilized by SPNPs were stable for at least 20 days at room temperature, whereas the emulsion that was stabilized by SPI showed a significant creaming and phase separation phenomenon. The SPNPs also showed a higher antioxidant and reducing effect compared to SPI. The use of mTG induced cross-linking resulted in the formation of covalent bonding between protein molecules, and led to the formation of nanoparticles with higher stability. The approaches support the utilization of inexpensive and abundant plant-based resources as emulsion stabilizers in food applications.