Understanding how dietary patterns influence chronic kidney disease (CKD) development is crucial for effective prevention strategies. This study identified distinct dietary patterns among Korean adults and investigate their association with CKD development. This retrospective cohort study used data from the Korean Genome and Epidemiology Study health examinee study database of community-dwelling adults aged ≥40 years in South Korea (2004–2016). Then, dietary patterns were identified using K-means clustering analysis based on the weights of 106 foods and intakes of energy and 22 nutrients. The dependent variable for cox regression analyses was the development of new-onset CKD, defined as an estimated glomerular filtration rate <60 mL/min/1.73 m² during follow-up. A total of 57,213 participants were classified into three dietary clusters. Cluster C, characterized by lower overall food, energy, and nutrient intake and higher carbohydrate intake, was independently associated with increased CKD risk (adjusted hazard ratio [aHR], 1.59; 95% confidence interval [CI], 1.04–2.41; P = 0.031) compared to Cluster A, characterized by higher intake of vegetables and fish/shellfish. Subgroup analyses revealed that Cluster C still had a significantly higher risk for CKD development in the groups of age ≥65 years (aHR, 3.58; 95% CI, 1.31–9.77; P = 0.013), male (aHR, 2.00; 95% CI, 1.08–3.71; P = 0.028), previous cardiovascular disease (aHR, 4.62; 95% CI, 1.08–19.72; P = 0.039), systolic blood pressure ≥130 mmHg (aHR, 1.96; 95% CI, 1.08–3.56; P = 0.026), and body mass index ≥25 kg/m2 (aHR, 3.62; 95% CI, 1.48–8.84; P = 0.005). Both the quantity and quality of food intake may influence CKD development in Korean adults. Maintaining a balanced, nutrient-rich diet could be key for CKD prevention, especially in high-risk subgroups.