Autoimmune disorders like type 1 diabetes (T1D) are complex diseases caused by numerous factors including both genetic variance and environmental influences. Two such exogenous factors, intestinal microbial composition and enterovirus infection, have been independently associated with T1D onset in both humans and animal models. Since environmental factors rarely work in isolation, we examined the cross-talk between the microbiome and Coxsackievirus B4 (CVB4), an enterovirus that accelerates T1D onset in non-obese diabetic (NOD) mice. We demonstrate that CVB4-infection induced restructuring of the intestinal microbiome prior to T1D onset that was associated with thinning of the mucosal barrier, bacterial translocation to the pancreatic lymph node, and increased detection of circulating and intestinal commensal-reactive antibodies. Notably, the CVB4-induced change in community composition was strikingly similar to that of uninfected NOD mice that spontaneously developed diabetes, thus implying a mutual diabetogenic microbiome. Furthermore, fecal microbiome transfer (FMT) of the diabetogenic microbiota from CVB4-infected mice was sufficient to enhance T1D susceptibility in naive NOD recipients. These findings support a model whereby CVB infection disrupts the microbiome and intestinal homeostasis in a way that promotes activation of autoreactive immune cells and T1D.