A lower BMI has been reported among consumers of organic foods, but this relationship has never been examined in a prospective design study. Our aim was to prospectively investigate the association between frequency of organic food consumption and weight change. We analysed data from 62 224 participants of the NutriNet-Santé cohort (78 % women, mean age=45 years) with information on consumption frequency of organic foods, dietary intake and repeated anthropometric data. For sixteen products, participants reported their consumption frequency of labelled organic foods (never, occasionally, most of the time). An organic score (OS) with a maximum of thirty-two points was computed. The associations of the OS (modeled as quartiles (Q)) with change in BMI during follow-up (on average 3·1 years) and with the risk of overweight and obesity were estimated by ANCOVA and multivariable logistic regression. A lower BMI increase was observed across quartiles of the OS (mean difference Q4 v. Q1=−0·16 (95 % CI −0·32, −0·01). An increase in the OS was associated with a lower risk of overweight and obesity (among non-overweight and non-obese participants at inclusion): OR for Q4 v. Q1 were 0·77 (95 % CI 0·68, 0·86) and 0·69 (95 % CI 0·58, 0·82), respectively. Concerning obesity risk, the association was stronger among participants with higher adherence to nutritional guidelines. This study supports a strong protective role of consumption frequency of organic foods with regard to the risk of overweight and obesity that depends on overall dietary quality. Upon confirmation, these results may contribute to fine-tune nutritional guidelines by accounting for farming practices in food production.