Epidemiological research confirms that prevalence of suboptimal micronutrient intake across Europe is an emerging concern of public health. Our aim was to investigate the association between a new index of carbohydrate quality and micronutrient adequacy in the “Seguimiento Universidad de Navarra (SUN)” cohort. The baseline assessment expanded from 1999 to March 2012. We assessed 16841 participants who completed a validated 136-item semi-quantitative FFQ at baseline. We created a new index to evaluate the carbohydrate quality following 4 criteria: dietary fiber intake, glycemic index (GI), whole grains /total grains ratio and solid carbohydrates/ total carbohydrates ratio. Subjects were classified into quintiles according to this index. We evaluated the intake of: zinc, iodine, selenium, iron, calcium, potassium, phosphorus, magnesium, chromium and vitamins B1, B2, B3, B6, B12, C, A, D, E and folic acid. The probability of intake adequacy was evaluated using the estimated average requirements (EAR)-cut point and the probabilistic approach. Logistic regression analysis was used to assess the nutritional adequacy according to the carbohydrate quality index (CQI).Participants in the highest quintile of CQI showed the lowest prevalence of inadequacy. A higher quality of carbohydrate intake was associated with lower risk of nutritional inadequacy in comparison with the lowest quintile of CQI (adjusted OR: 0•06; 95 % CI: 0•02, 0•16; P for trend <0•001. A higher CQI was strongly associated with a better micronutrient adequacy in a young Mediterranean cohort, stressing the importance of focusing nutritional education not only in carbohydrates quantity, but also in quality.