There is scarce research focusing on the relationship between the low-carbohydrate dietary score and the development of a metabolically unhealthy phenotype. Therefore, this cohort study was designed to assess the association between the low-carbohydrate dietary score and the risk of metabolically unhealthy phenotypes (MUP). This study included 1299 adults with healthy metabolic profiles who were followed for 5.9 years. Results indicated an inverse association between the second tertile of the low-carbohydrate dietary score and the risk of developing metabolically unhealthy obesity (MUO) (HR: 0.76, 95% CI: 0.59-0.98). In addition, we found an inverse association between the healthy low-carbohydrate dietary score and the risk of MUO (HR: 0.77, 95% CI: 0.60-0.99). Our results revealed a nonlinear inverse association between the low-carbohydrate dietary score and the risk of MUP only in subjects with overweight or obesity. This relationship was independent of animal protein and fat intake. Also, we found that a lower intake of unhealthy carbohydrates was associated with a lower risk of MUP only in subjects with overweight or obesity.