Background Many genetic variants show highly robust associations with body mass index (BMI). However, the mechanisms through which genetic susceptibility to obesity operate are not well understood. Potentially modifiable mechanisms, including eating behaviors, are of particular interest to public health. Objective Here we explore whether eating behaviors mediate or modify genetic susceptibility to obesity. Design Genetic risk scores for BMI (BMI-GRS) were calculated for 3515 and 2154 adults in the Fenland and EDEN population-based cohort studies, respectively. The eating behaviors: emotional eating, uncontrolled eating and cognitive restraint, were measured using a validated questionnaire. The mediating effect of each eating behavior on the association between the BMI-GRS and measured BMI was assessed using the Sobel test. Additionally, we tested for interactions between each eating behavior and the BMI-GRS on BMI. Results The association between the BMI-GRS and BMI was mediated by both emotional eating (EDEN: P-Sobel=0.01; Fenland: P-Sobel=0.02) and uncontrolled eating (EDEN: P-Sobel=0.04; Fenland: P-Sobel=0.0006) in both sexes combined. Cognitive restraint did not mediate this association (P-Sobel>0.10), except amongst EDEN women (P-Sobel=0.0009). Cognitive restraint modified the relationship between the BMI-GRS and BMI amongst men (EDEN: P-interaction=0.0001; Fenland: P-interaction=0.04) and Fenland women (P-interaction=0.0004). By tertiles of cognitive restraint, the association between the BMI-GRS and BMI was strongest in the lowest tertile of cognitive restraint, and weakest in the highest tertile. Conclusions Genetic susceptibility to obesity was partially mediated by the ‘appetitive’ eating behavior traits (uncontrolled and emotional eating) and, in three of the four population groups studied, was modified by cognitive restraint. High levels of cognitive control over eating appear to attenuate the genetic susceptibility to obesity. Future research into interventions designed to support restraint may help to protect genetically susceptible individuals from weight gain.