Fermenting garlic and onion provides the advantages of storage life extension, anti-oxidative and anti-diabetic activities, and their metabolite, allyl mercaptan, offers a strong aroma and various health benefits. Here, we report the probiotic properties of Lactobacillus pentosus SMB718 isolated from Korean traditional paste and its high allyl mercaptan productivity in garlic and onion fermentation. This strain was safe for use in food fermentation, as it was a non-biogenic amine producer and non-hemolytic. It showed high stability under simulated human gastrointestinal conditions and good adhesion ability to intestinal epithelial cells, including both Caco-2 and HT-29. This strain had antioxidant and anti-microbial activities. In addition, the heat-killed cells and lysate exerted anti-inflammatory effects on both LPS-stimulated RAW 264.7 cells and mouse macrophages by inhibition of pro-inflammatory cytokines and induction of anti-inflammatory cytokines. Furthermore, this strain possessed good fermentation properties in garlic and onion-enriched radish juice (GORJ); it grew well decreasing the pH and provided a rich aroma compound during fermentation. When L. pentosus SMB718 was used as a starter in garlic and onion fermentation, a significantly higher amount of allyl mercaptan (344 ppb) was produced compared with that produced by the type strain (82 ppb). In conclusion, L. pentosus SMB718 can be used as a beneficial probiotic starter for better flavor production in the fermentation of allium species plants.