Although micronutrient deficiencies affect 2 billion people worldwide, no index focuses on measuring the risk of overt nutrient deficiency. We aimed to develop an index that could capture the nutrient dimension of nutritional security, a nutrient security index (named SecDiet), and evaluate its apparent validity. The SecDiet (range: 0–1) is based on the square-weighted average of the probabilities that the intake of twelve critical nutrients exceeds the threshold value associated with a risk of overt deficiency. Using adult populations from a French representative survey (INCA3, n 1774) and a large cohort (NutriNet-Santé, n 104 382), the content and construct validity of the SecDiet was evaluated by estimating associations of the SecDiet with its components and with relevant socio-demographic characteristics. The SecDiet was high in the overall population (0·93 (SD 0·09) in INCA3) and markedly skewed towards 1 (i.e. lower risk of insufficient intake). It correlated positively with its twelve components (r 0·17–0·78, all P < 0·001). The SecDiet was associated with monthly income (P = 0·002), perception of financial situation, professional situation, food insufficiency and security statuses (all P < 0·001) in the INCA3 population and with monthly income, professional situation and level of education (all P < 0·001) in the NutriNet-Santé population. Unlike a broader nutrient-based quality index taken as comparison, the SecDiet mean decreased and the tail of its distribution notably extended downwards in at-risk sub-populations, thus revealing its specific sensitivity. The SecDiet could be used to screen sub-groups or study the determinants of nutrient insecurity in large population surveys.