Abstract Purpose This study attempted gaining insight into the intake of protein and fat of 12- to 36-month-old children in the Netherlands. Methods In 2017, a Total Diet Study (TDS) was carried out in the Netherlands including following three age groups: 12–17-, 18–23- and 24- to 36-month-old children. Protein and fat concentrations of 164 composite samples were analysed and combined with the consumption data from the Dutch National Food Consumption Survey 2012–2016 (DNFCS). Results Median protein intake of the 12- to 35-month-old Dutch children based on the TDS was 35 g/day with main contributions from the food subgroups “milk and milk-based beverages”, “beef” and “yoghurts and desserts”. Median fat intake was 34 g/day with main contributions from the food subgroups “margarines”, “cheeses” and “milk and milk-based beverages”. For the youngest age group (12- to 18-month-old children), (ready to drink) follow-on formula was one of the main contributors to the fat intake. Conclusion Compared to the EFSA reference values, protein intake of the Dutch 12- to 36-month-old children is high, whereas fat intake follows the reference intake. A TDS is a suitable instrument to estimate macronutrient intakes.