Seeds are usual source of contamination and their sprouts are commonly associated foodborne illness. Therefore, the aim of this study was to evaluate the antibacterial vapor phase efficiency of allspice, thyme and rosemary essential oils on two foodborne pathogens in in vitro and on alfalfa seeds, including the chemical profile of the tested EOs and their effect on the sensory characteristics of the sprouts. Antibacterial activity was determined through the minimal inhibitory concentration (MIC) of EOs in vapor phase to inhibit the growth of Listeria monocytogenes and Salmonella Typhimurium in culture media and on alfalfa seeds. Also, the germination and the effect on sensory characteristics of the sprouts were determined. Thyme EO was the most effective of the tested EOs on culture media and on alfalfa seeds, against both bacteria. When rosemary EO was tested against L. monocytogenes in alfalfa seeds, the MIC (4.0 mL/L) was higher, compared to the one obtained in culture media (2.7 mL/L). But when this EO was tested against S. Typhimurium, the MIC in alfalfa seeds was lower than in culture media (11.7 vs 13.3 mL/L). Allspice EO resulted more effective against both bacteria in alfalfa seeds (6.0 mL/L for L. monocytogenes and 6.7 mL/L for S. Typhimurium), compared to culture media (12.0 mL/L for L. monocytogenes and 13.3 mL/L for S. Typhimurium). Vapor phase EOs MICs resulted in significant (p ≤ 0.05) decreases of L. monocytogenes and S. Typhimurium counts compared to the control. There also was a significant (p ≤ 0.05) difference between systems (in vitro or on alfalfa seeds) despite the microorganism or the evaluated EO. Treatment alfalfa seed with vapor phase EOs, did not affect the seed germination. Sensory acceptability of the sprouts, obtained of treated seeds, did not were significant (p ≥ 0.05) different of the sprouts obtained from the non-treated seeds.