Microbial detoxification, as an environmentally friendly strategy, has been widely applied for benzo[a]pyrene (BaP) degradation. Within this approach, food-derived microbial strains offer unique advantages in safety, specificity, and sustainability for detoxifying food-borne BaP. In this study, we aimed to explore the potential of such strains in BaP degradation. TC-5, a strain that degrades BaP, was isolated from kefir grains. Surprisingly, 12 genes encoding dehydrogenases, synthases, and oxygenases, including , , , , and , which are related to BaP degradation, were up-regulated by 2.01-fold to 4.52-fold in TC-5. Two potential degradation pathways were deduced. In pathway I, dioxygenase, betaine aldehyde dehydrogenase, and beta-ketoacyl-ACP synthase III FabHB act sequentially on BaP to form 4H-pyran-4-one,2,3-dihydro-3,5-dihydroxy-6-methyl via the phthalic acid pathway. In the presence of the cytochrome P450 enzyme, BaP progressively mediates ring cleavage via the anthracene pathway, eventually forming 3-methyl-5-propylnonane in pathway II. Notably, TC-5 achieved an impressive BaP removal efficiency of up to 63.94%, with a degradation efficiency of 32.89%. These results suggest that TC-5 has significant potential for application in addressing food-borne BaP contamination. Moreover, our findings expand the application possibilities of Xinjiang fermented milk products and add to the available green strategies for BaP degradation in food systems.