We aimed to investigate associations of dietary intakes with unhealthy metabolic phenotype development, in normal weight and overweight/obese adults separately. A total of 1114 individuals, aged ≥19 years, with healthy phenotype in the third examination cycle of Tehran Lipid and Glucose Study were followed until the fifth examination. Dietary intakes were estimated using the food frequency questionnaires, collected during the study. The participants were grouped as normal weight and overweight/obese according to the baseline body mass index (BMI). Unhealthy metabolic status was determined as having more than one component of metabolic syndrome using the Joint Interim Statement. Regardless of BMI, higher intakes of magnesium, dairy products, poultry, apples/pears, citrus fruits, and tea/coffee decreased the risk of developing unhealthy phenotype, while higher intakes of fast foods, organ meats, and potatoes increased the risk. Food intake can influence the transition to unhealthy phenotype in metabolically healthy adults, irrespective of the BMI status.