Insulin, a critical metabolic hormone to maintain blood glucose homeostasis, is synthesized and folded in the endoplasmic reticulum (ER) of pancreatic β-cells as the insulin precursor proinsulin (ProIns). ProIns misfolding and aggregation detected in diabetic β-cells induces ER stress and obstructs normal trafficking, processing, and secretion of insulin, which eventually can result in pancreatic β-cell dedifferentiation and death. We have developed quantitative methods to measure misfolded and aggregated ProIns in β-cells by utilizing ProIns oligomer-specific ELISA and proximity ligation assay. Under conditions of induced ER stress, both assays detected significant accumulation of aggregated ProIns in β-cells. ProIns aggregation was also observed in isolated pancreatic islets cultured at high glucose levels. Moreover, high glucose in β-cells downregulated expression of genes mediating clearance of misfolded proteins from the secretory pathway through ER autophagy and ER-associated protein degradation. Inhibition of autophagy in β-cells induced strong induction of misfolded ProIns accumulation, whereas ER-associated degradation inhibition was not effective in generating ProIns aggregates. Finally, we observed subcellular colocalization of aggregated ProIns with protein markers of autophagosomes. Our results indicate that autophagy controls degradation of aggregated misfolded ProIns under conditions of hyperglycemia and diabetes.