In Brazil, children’s eating patterns have been characterised by an increased consumption of ultra-processed foods that are fortified. Our aims were to (1) estimate the prevalence of inadequate micronutrient intake among children from low-income families and (2) to assess micronutrient intake from fortified foods. We carried out a cross-sectional study from a randomised field trial conducted at healthcare centres in Porto Alegre, Brazil, with 446 mother–child pairs, with the children aged 2–3 years. Dietary data were assessed using two 24-h recalls. The prevalence of inadequacy for six micronutrients was estimated using the proportion of individuals with intakes below the estimated average requirement (EAR). Micronutrient intakes from fortified foods were evaluated using EAR and upper tolerable level (UL). Healthy foods consumption was below the recommendations, except for beans, and 88·1 % of the children consumed ultra-processed foods. A low prevalence of inadequate micronutrient intake was observed for Fe (1·2 %), vitamin C (4·7 %), vitamin A (5·2 %), Ca (11·4 %) and folate (15·2 %). None of the children had intakes less than the EAR for Zn. Fortified foods contributed between 11·3 and 38·3 % to micronutrient intakes, and 43·0 % of the children met the EAR for Fe, 13·9 % for vitamin C and 12·3 % for Zn using fortified foods only. In addition, 4·0 % of the children exceeded the UL for vitamin A, 3·1 % for Zn, 1·1 % for folic acid and 0·2 % for Fe. These results highlight a low prevalence of inadequate micronutrient intakes among children and suggest that such a group could be at risk of excessive micronutrient intakes provided by ultra-processed foods.