Aim: To investigate the association between organic food consumption and the incidence of type 2 diabetes mellitus. Methods: Among 41,286 cohort participants, aged 50–65 years, organic food consumption of vegetables, fruits, dairy products, eggs, meat, and cereal products, was summarized into an organic food score evaluated as never, low, medium and high consumption and as continuous intake. During follow-up, 4,843 cases were identified in the National Diabetes Register. Organic food consumption was associated to the disease incidence in Cox regression models. Results: Organic food consumption was linearly associated with a lower incidence of type 2 diabetes mellitus (Women, HR: 0.94, 95% CI: 0.89–1.00, Men, HR: 0.95, 95% CI: 0.90–1.00). Organic food consumption frequency, compared to never consumption, showed HRs below 1.00 for both women (medium intake HR: 0.96, 95% CI: 0.84–1.10, high intake HR: 0.88, 95% CI: 0.74–1.05) and men (low intake, HR: 0.95, 95% CI: 0.85–1.05, medium intake, HR: 0.92, 95% CI: 0.83–1.03, high intake, HR: 0.89, 95% CI: 0.75–1.05) but were not statistically significant. Similar patterns were observed with consumption of the specific organic food groups for women, but not for men. Conclusions: Organic food consumption was associated with a suggested lower incidence of type 2 diabetes mellitus.