Selective immunoglobulin A (IgA) deficiency (SIgAD) is the most common primary immunodeficiency disease with a prevalence of about 1:500 individuals. SIgAD is heterogeneous, though thought to be due to a defect in the differentiation of IgA-bearing B lymphocytes into IgA-secreting plasma cells which provide a first line of defense against bacterial and viral pathogens. Although SIgAD was for a long time considered asymptomatic, longitudinal studies have revealed that about 80% of patients are symptomatic and can present with a range of phenotypes including allergic disease, recurrent bacterial respiratory tract infections, gastrointestinal disorders, and autoimmune diseases. Secretory IgA has been shown to play a critical role in maintaining immune homeostasis in the gut by determining the composition of and directing the function of gut microbiota. Patients with SIgAD demonstrate gut dysbiosis with enriched proinflammatory phyla that is only partially compensated for by IgM and IgG. In this review, we will discuss what is known about the microbiome of individuals with SIgAD and how this might provide insights into therapeutics and monitoring in these patients.