Tissue resident macrophages are found at birth in the islets of Langerhans of all strains of mice examined. To examine the macrophage’s role in islet homeostasis and diabetogenesis, we depleted the cells using a monoclonal antibody against the CSF-1 receptor. Depletion of islet macrophages in the C57BL/6 mouse strain for 2–6 weeks did not affect multiple parameters of homeostasis including glucose tolerance, insulin content, or whole islet transcriptome. In contrast, depletion of the islet macrophages in 3 week old diabetes-prone NOD mice led to multiple changes in the progression of disease. First, there was a reduction in CD4 T cells and dendritic cells that infiltrate islets at 4–6 weeks of age. Second, there was a reduction in the presentation of insulin-derived peptides to T cells by dispersed islet cells. Third, the development of autoimmune diabetes was significantly reduced. The protection from diabetes induced by anti-CSF-1 receptor antibody was effective even when treatment was started at 10 weeks of age, a time where NOD mice have significant infiltration in their islets. Despite the protection from diabetes, mice treated with anti-CSF-1 receptor antibody at both 3 and 10 weeks of age harbored extensive leukocytic infiltration into islets when examined at 20–40 weeks of age. Treatment with an anti-PD-1 antibody led to immediate diabetes progression in all of the long-term protected NOD mice. These results show that depletion of islet-resident macrophages limited the islet leukocytic infiltration in the early phase of diabetogenesis and also permitted the establishment of a long-lived protective regulatory milieu late in the disease.