Introduction: Fruit and vegetable (FV) consumption can be a protective factor for chronic diseases, but few studies have investigated the association between FV consumption and health risks for chronic disease in the context of the food and nutrition assistance system. The aim of this study was to assess the association between FV consumption and the prevalence of hypertension, type 2 diabetes mellitus, and body mass index (BMI) among food pantry users in small- to mid-sized metropolitan communities in the northeastern United States. Methods: We used data from three health surveys conducted among residents of communities in upstate New York to construct a predictive model of food pantry use. We then applied the model to a regional subset of SMART Behavioral Risk Factor Surveillance System (BRFSS) data collected in the northeastern United States to identify potential food pantry users. We examined the associations between FV intake and diabetes, hypertension, and BMI through univariate and multivariate logistic and linear regressions. Additionally, we investigated food pantry use as a potential modifier of these associations. Results: The analysis dataset included 5,257 respondents, of which 634 individuals (12.06%) were estimated to be food pantry users. Vegetables consumption was associated with decreased odds of hypertension and lower BMI, regardless of food pantry use. Fruits consumption was associated with decreased odds of diabetes regardless of food pantry use. The association between fruit consumption and BMI was modified by the use of food pantry. Among food pantry users, consumption of fruits was associated with a higher BMI, while among food pantry non-users, it was associated with a lower BMI. Conclusion: The overall protective effect of increased FV consumption on chronic disease risks suggest that increasing FV availability in food pantries may not only alleviate hunger but also contribute to better health. Further research is needed to elucidate what is driving the discrepant association between fruit consumption and BMI among food pantry users and non-users.