Background B lymphocytes are an important cell population of the immune regulation; their role in the regulation of food allergy has not been fully understood yet. Objective This study aims to investigate the role of a subpopulation of tolerogenic B cells (TolBC) in the generation of regulatory T cells (Treg) and in the suppression of food allergy‐induced intestinal inflammation in mice. Methods The intestinal mucosa‐derived CD5+ CD19+ CX3CR1+ TolBCs were characterized by flow cytometry; a mouse model of intestinal T helper (Th)2 inflammation was established to assess the immune regulatory role of this subpopulation of TolBCs. Results A subpopulation of CD5+ CD19+ CX3CR1+ B cells was detected in the mouse intestinal mucosa. The cells also expressed transforming growth factor (TGF)‐β and carried integrin alpha v beta 6 (αvβ6). Exposure to recombinant αvβ6 and anti‐IgM antibody induced naive B cells to differentiate into the TGF‐β‐producing TolBCs. Coculturing this subpopulation of TolBCs with Th0 cells generated CD4+ CD25+ Foxp3+ Tregs. Adoptive transfer with the TolBCs markedly suppressed the food allergy‐induced intestinal Th2 pattern inflammation in mice. Conclusions CD5+ CD19+ CX3CR1+ TolBCs are capable of inducing Tregs in the intestine and suppress food allergy‐related Th2 pattern inflammation in mice.