This study investigated the stability and antimicrobial activity of allyl isothiocyanate (AITC) in medium chain triglyceride (MCT) or soybean oil (SBO) dispersed in an oil-in-water (o/w) system during long-term storage. Oil type, content, and oxidative stability affect the stability and antimicrobial activity of AITC during storage. High oil content is favorable for AITC stability in the emulsion. Notably, AITC with MCT is more stable than AITC with SBO with the same oil content. Consequently, AITC with MCT is more effective than AITC with SBO in inhibiting G(-) bacteria (E. coli O157:H7, Salmonella enterica, and Vibrio parahaemolyticus) and G(+) bacteria (Staphylococcus aureus and Listeria monocytogenes).