Recent epidemiological studies have explored the association between organic food consumption and the risk of obesity, but the results remain controversial. A systematic review and meta-analysis were conducted to determine the association between organic food consumption and the risk of obesity. Rigorous methods for a comprehensive search were employed to search for literature in PubMed/MEDLINE, Web of Science, and Embase for relevant articles published until 30 November 2021. Pooled odds ratio (OR) with 95% confidence intervals (Cis) were calculated using a DerSimonian and Laird random-effects model to understand the risk of obesity based on exposure to organic food. Four studies, comprising 104,488 healthy subjects and 39,425 adults who consumed organic food, reported 1625 incident cases of obesity. Compared with the unexposed group, organic food consumption was associated with a lower probability of obesity (OR: 0.89, 95% CI: 0.80–0.97, p < 0.001). Subgroup analysis showed that this association was higher in the cohort (OR: 0.78, 95% CI: 0.63–0.92) than cross-sectional studies (OR: 0.95, 95% CI: 0.91–1.00), respectively. Overall, organic food consumption had a modest reduction (11%) in the risk of obesity and can be an appropriate strategy to prevent obesity.