Over the past decade, demand has increased for natural, minimally processed produce, including sprout-based products. Sanitization with 20,000 ppm of calcium hypochlorite is currently recommended for all sprouting seeds before germination to limit sprout-related foodborne outbreaks. A potentially promising disinfectant as an alternative to calcium hypochlorite is acidified spontaneous essential oil nanoemulsions. In this study, the efficacy of an acidified carvacrol nanoemulsion was tested against mung beans and broccoli seeds artificially contaminated with a Salmonella enterica Enteritidis cocktail (ATCC BAA-709, ATCC BAA-711, and ATCC BAA-1045). Treatments were performed by soaking inoculated seeds in acidified (50 mM acetic or levulinic acid) carvacrol nanoemulsions (4,000 or 8,000 ppm) for 30 or 60 min. After treatment, the number of surviving cells was determined via plate counts and/or the most probable number (MPN) approach. Treatment for 30 min successfully reduced Salmonella Enteritidis by 4 log CFU/g on mung beans (from an initial contamination level of 4.2 to 4.6 log CFU/g) and by 2 log CFU/g on broccoli seeds (from an initial contamination level of 2.4 to 2.6 log CFU/g) to below our detection limit (≤3 MPN/g). Treated seeds were sprouted and tested for the presence of pathogens and sprout yield. The final sprout product had no detectable pathogens, and total sprout yield was not influenced by any treatment.