ScopeThis study evaluates the potential of bioconverted garlic ferments (BGFs) to stimulate the intestinal immune system and modulate cecal microbiota composition.Methods and resultsIn vitro, BGF significantly enhances Peyer's patch (PP)‐mediated bone marrow cell proliferation and increases the production of interferon‐gamma (IFN‐γ), granulocyte macrophage‐colony stimulating factor (GM‐CSF), interleukin (IL)‐6, and immunoglobulin A (IgA) but not IL‐4, IL‐5, and immunoglobulin E (IgE). Oral administration of BGF to C3H/HeN mice for 4 weeks significantly increases the GM‐CSF (42.1–45.8 pg mL−1) and IFN‐γ (6.5–12.1 pg mL−1) levels in PP cells. BGF also significantly elevates the levels of tumor necrosis factor‐alpha (TNF‐α, 165.0–236.3 pg mg−1), GM‐CSF (2.4–3.0 ng mg−1), and IFN‐γ (1.5–3.2 ng mg−1) in the small intestinal fluid, and TNF‐α (2.2–3.1 pg mL−1) and IFN‐γ (10.3–0.21.5 pg mL−1) in the mouse serum. Cecal microbial analysis reveals that BGF increases Bacteroidota and Verrucomicrobiota and decreases Actinobacteria and Bacillota at the phylum level in mice. At the genus level, BGF significantly increases the abundance of Fusimonas (250 mg kg−1 BW−1 day−1), Bacteroides (125 and 250 mg kg−1 BW−1 day−1), and Akkermansia (125 mg kg−1 BW−1 day−1) and decreases that of Bifidobacterium (62.5 and 250 mg kg−1 BW−1 day−1) and Limosilactobacillus (125 and 250 mg kg−1 BW−1 day−1).ConclusionThis study provides the first evidence of BGF's ability to modulate the intestinal immune system and gut microbiota, supporting its potential as a novel functional material to enhance gut immunity.