Abstract Purpose This study investigates intakes of risk micronutrients from non-fortified foods, fortified foods and food supplements in different age and gender sub-groups of the Dutch population. Methods This is a secondary analysis of the Dutch National Food Consumption Survey (DNFCS 2012–2016, N = 4313, 1–79 years). The proportion of the population with Habitual Intakes below the Estimated Average Requirement (EAR) and above the Upper Level (UL) for calcium, iron, zinc, vitamin A, vitamin B6, folate, vitamin D and vitamin E from non-fortified foods, fortified foods and total intake including food supplements was calculated using Statistical Program to Assess Dietary Exposure (SPADE). Results More than 50% of the population had an intake below the EAR for calcium, iron, vitamin D and folate. Intakes were inadequate for certain sub-groups for the other vitamins and minerals. Adolescents and women were the population sub-groups most likely to have an intake below the EAR. For zinc, vitamin A and folic acid, more than 1% of toddlers exceeded the UL from the total intake. A negligible proportion exceeded the UL for the other vitamins and minerals. Conclusion Inadequate intakes were found for several micronutrients in various population sub-groups despite an apparently well-nourished population. Intakes of zinc, folic acid and vitamin A from food supplements in toddlers and preschoolers should be investigated further to ensure they do not exceed recommended amounts. These results can be used to inform policy makers and to design nutritional interventions to improve micronutrient intakes in the Netherlands.