Background: The organic food market has grown rapidly worldwide in the past 15 years. However, evidence concerning the health effects of organic foods is scarce. We evaluated the cross-sectional association of organic food purchase, as a proxy of organic food consumption, with diabetes in a nationally representative population. Methods: We included 8199 participants aged ≥20 years from the National Health and Nutrition Examination Survey 2007–2008 and 2009–2010. Organic food purchase and frequency were ascertained by questionnaires. Diabetes was defined as a self-reported physician diagnosis or a hemoglobin A1c level ≥6.5% or both. We used logistic regression with sample weights to estimate the odds ratios (ORs) and 95% confidence intervals (CIs). Results: Individuals who reported purchasing organic foods were less likely to have diabetes compared to those who did not report organic food purchase. After adjustment for age, gender, race/ethnicity, family history of diabetes, socioeconomic status, and dietary and lifestyle factors, the OR of diabetes associated with organic food purchase was 0.80 (95% CI 0.68–0.93). The association remained significant after additional adjustment for BMI with OR of 0.80 (0.69–0.94). Conclusions: In a nationally representative population, frequent organic food purchase was inversely associated with diabetes prevalence in adults in the United States.