Abstract Primary immunodeficiencies are heritable disorders of the immune response that most commonly manifest as an inability to generate immunoglobulin A (IgA). Despite its prevalence, IgA deficiency is considered a benign form of antibody deficiency due to a lack of easily observed clinical symptoms. CD19 is an important co-receptor that facilitates B cell receptor signaling and B cell development into antibody-secreting plasma cells. CD19 deficiency is a known genetic risk factor for the development of common variable immunodeficiency (CVID). Here, we utilize the CD19−/− mouse model to quantify the role of IgA deficiency on gut homeostasis. Our results indicate that CD19−/− mice develop a severe gut IgA deficiency associated with aberrant anti-commensal IgA responses that result in the outgrowth of anaerobic bacteria in the gut. More importantly, anaerobic expansion results in intestinal malabsorption under steady-state conditions. Intestinal malabsorption is associated with defects in normal hepatobiliary circulation, vitamin deficiency, and dyslipidemia. Additionally, results from histological analysis and RNAseq experiments indicate that CD19−/− mice develop intestinal epithelial cell (IEL) lymphocytosis mediated by CD8aa+TCRgd lymphocytes. Finally, CD19−/− mice, while deficient in anti-gliadin antibody (AGA) production compared to WT mice, demonstrate a significantly stronger relationship between serum AGA titers and total serum IgG and IgA production compared to WT animals and have significantly elevated ileal expression of tissue transglutaminase 2. Collectively, we believe that we have identified a novel mouse model of sero-negative celiac disease that will be of great value to the celiac research community.