Type 1 diabetes (T1D) results from a T cell dependent, autoimmune destruction of insulin producing beta cells in pancreatic islets of Langerhans, which results in insulin deficiency despite attempts at beta cell replacement by the emergence of newly-differentiated beta cells throughout T1D development. The origin of these cells has been difficult to assess as these are rapidly destroyed by the underlying autoimmunity. The identification of islets of Langerhans is typically assessed by either immunochemistry or immunofluorescence using antibodies directed against the different signature hormones and surface markers of various endocrine cells. However, the limited number of markers that can be used simultaneously and the uneven spatial distribution of endocrine cells within islets, limit the use of these histological analyses. To circumvent these caveats, we developed a novel approach using multi-parametric flow cytometry to assess the phenotype and function of pancreatic islet cell populations throughout T1D development. Using such strategy, we show that while beta cells undergo autoimmune destruction, insulin-producing cells arise from trans-differentiated alpha or delta cells, an outcome that was not solely the result of beta cell self-renewal. Moreover, we show that CD4(+)T cell-mediated inflammation correlates with the emergence of this insulin-producing beta cell-like cell.