Immunoglobulin A (IgA) exerts its primary function at mucosal surfaces where it binds microbial antigens to regulate bacterial growth and epithelial attachment. One-third of individuals with IgA deficiency (IgAD) suffer from recurrent mucosal infections, possibly related to an altered microbiota. We here aimed to delineate the impact of IgA deficiency and the IgA-autoantibody status on the composition and functional capacity of the gut microbiota.