Oil-in-water (O/W) 'Yuja' nanoemulsion was successfully prepared using 'Yuja' juice as an aqueous phase and 'Yuja' seed oil as an oil phase. 'Yuja' nanoemulsion was further coated using chitosan solution to improve its stability. Firstly, 'Yuja' oils were extracted from traditionally wasted 'Yuja' seeds by using supercritical carbon dioxide extraction technique. The mean particle diameter of 'Yuja' nanoemulsion was 145.6 nm and significantly (p<0.05) decreased to 79.5 nm after chitosan coating. The shape of 'Yuja' nanoemulsion droplets was heterogeneous with some round and rod shapes whereas chitosan-coated 'Yuja' nanoemulsion showed homogenous droplets with spherical shape and uniform distributions. Antimicrobial activity of ultrasonic homogenized 'Yuja' juice (UH-'Yuja' juice), 'Yuja' nanoemulsion ('Yuja' NE) and chitosan-coated 'Yuja' nanoemulsion (CS-'Yuja' NE) was evaluated against Staphylococcus aureus and Escherichia coli at 25℃ and 10℃ in every 2 h up to 12 h. Antimicrobial activity of UH-'Yuja' juice, 'Yuja' NE, and CS-'Yuja' NE was significantly (p<0.05) different compared to the negative control (PBS) both at 25℃ and 10℃ and similar to the positive control (Ampicillin) at 10℃. These results showed that CS-'Yuja' NE had higher antimicrobial activity than UH-'Yuja' juice and 'Yuja'-NE against Staphylococcus aureus and Escherichia coli.