The interrelationship between IgAs and microbiota diversity is still unclear. Here we show that BALB/c mice had higher abundance and diversity of IgAs than C57BL/6 mice and that this correlated with increased microbiota diversity. We show that polyreactive IgAs mediated the entrance of non-invasive bacteria to Peyer’s patches, independently of CX3CR1+ phagocytes. This allowed the induction of bacteria-specific IgA and the establishment of a positive feedback loop of IgA production. Cohousing of mice or fecal transplantation had little or no influence on IgA production and had only partial impact on microbiota composition. Germ-free BALB/c, but not C57BL/6, mice already had polyreactive IgAs that influenced microbiota diversity and selection after colonization. Together, these data suggest that genetic predisposition to produce polyreactive IgAs has a strong impact on the generation of antigen-specific IgAs and the selection and maintenance of microbiota diversity. Display omitted •Different mouse strains have diverse predisposition to produce innate IgAs•Innate IgAs allow a controlled bacterial entrance•IgA-coated bacteria initiate a positive feedback loop of IgA production•IgA diversity results in microbiota diversification Reduced microbiota diversity has been associated with several pathologic conditions. Rescigno et al. show that the capacity to produce innate IgAs has an impact on microbiota diversity. IgAs can mediate the internalization of non-invasive bacteria and the initiation of a positive feedback loop of IgA production. IgA diversity might be a marker of a healthy condition.