To evaluate the impact of hurricanes Irma and María on the incidence of diabetes in Puerto Rico. Mortality increased substantially after hurricanes, but morbidity was not evaluated. We recruited 364 participants from the San Juan Longitudinal Study of Overweight Adults (SOALS) aged 40 to 65 who completed a three-year follow-up and who were free of diabetes. We conducted additional questionnaires between 1.7 and 2.5 years after the hurricanes. Glycosylated hemoglobin (HbA1c), fasting glucose and insulin were evaluated at all three visits. We compared the incidence of diabetes between visits prior to hurricanes and between visits that covered the hurricane period using the Generalized Estimated Equation Model (GEE), adjusting for repeated measures within the person, age and body mass index (BMI). The incidence of diabetes was significantly higher in the period covered by the hurricanes than in the period before them (multivariate GEE model: IRR = 2.1; 95% CI: 1.4—3.1). There was a significantly greater increase in the period covered by the hurricanes compared to the period prior to the Evaluation of the Homeostatic Insulin Resistance Model (HOMA-IR) (median: 0.3 IUU/ml vs. 0.2 IUU/ml). HbA1c levels increased by 0.4% in the period covered by the hurricanes. The increases in the incidence of diabetes, HOMA-IR and HbA1c were greater in the period covered by the hurricanes compared to the previous period. The increase in the incidence of diabetes remains significant after adjusting for age and BMI.