Abstract Background The aims of this study were to assess the intake of animal, plant and food group-specific protein, and to investigate their associations with socio-economic and lifestyle-related factors in Flemish preschoolers. Methods Three-day estimated dietary records were collected from 661 preschoolers aged 2.5-6.5 y (338 boys and 323 girls). Multiple linear regression analysis was used to investigate the association between animal, plant, and food group-specific protein intake and socio-economic and lifestyle factors. Results Animal proteins (mean 38 g/d) were the main source of total protein (mean 56 g/d), while mean plant protein intake amounted to 18 g/d. The group of meat, poultry, fish and eggs was the main contributor (51%) to animal protein intake, followed by milk and milk products (35%). Bread and cereals (41%) contributed most to the plant protein intake, followed by low-nutritious, energy-dense foods (21%). With higher educated fathers and mothers as reference, respectively, preschoolers with lower secondary and secondary paternal education had lower animal, dairy-, and meat-derived protein intakes, and those with lower secondary and secondary maternal education consumed less plant, and bread and cereal-derived proteins. Compared to children with high physical activity levels, preschoolers with low and moderate physical activity had lower animal and plant protein intakes. Significantly higher potatoes and grains-, and fish- derived proteins were reported for children of smoking mothers and fathers, respectively, compared to those of non-smoking mothers and fathers. Conclusions The total protein intake of Flemish preschoolers was sufficient according to the recommendations of the Belgian Superior Health Council. Parental level of education and smoking status might play a role in the sources of children's dietary proteins.