Background: There is growing evidence regarding the potential properties of nitrate-rich foods in development of chronic diseases. In this study, we investigated the association of nitrate-containing vegetables (NCVs) and the risk of chronic kidney disease (CKD). Methods: We evaluated 1546 eligible adult participants of the Tehran Lipid and Glucose Study (TLGS), at baseline (2006–2008) and again after 3 years (2009–2011). Dietary intake was collected using the validated semi-quantitative food frequency questionnaire. Nitrate-containing vegetables and its categories including high-, medium-, and low-nitrate vegetables were defined. Estimated glomerular filtration rate (eGFR) and CKD were defined. Association between NCVs and CKD in the cross-sectional phase and the predictability of NCVs consumption in CKD occurrence were assessed using multivariable logistic regression models with adjustment for potential confounders. Results: Mean dietary intake of energy-adjusted NCVs was 298.0 ± 177.3 g/day. Highest compared to the lowest tertile of NCVs was accompanied with a significantly lower mean eGFR (76.6 vs. 83.3, mL/min/1.73 m2, p < 0.001) and a higher prevalence of CKD (21.7 vs. 9.9%, p < 0.001). At baseline, higher intake of high-NCVs was associated with a 48% higher chance of having CKD (OR = 1.48, 95% CI = 1.05–2.13). After 3 years of follow-up, there was no significant association between consumption of total NCVs and its categories with the occurrence of CKD. Conclusion: Considering the lack of association between high-NCVs intakes and the risk of CKD in prospective analysis, additional research is recommended to clarify possible effect of nitrate intakes from vegetables on kidney function.