This study focused on the association between food insecurity and children's dietary intake in a representative sample of children in an area with high food insecurity in Duque de Caxias, Rio de Janeiro State, Brazil. This was a cross-sectional, population-based study with a probabilistic cluster sample of 402 families with children ranging from six to 30 months of age. Food insecurity was assessed based on the Brazilian Food Insecurity Scale (EBIA), and children's dietary intake was evaluated with two 24-hour recalls. Intake levels for food groups, energy, and nutrients were compared according to food insecurity status. Intake of sugar/sweets and fat was high, regardless of food insecurity status, and coffee intake was significantly higher among children with food insecurity. In the energy-adjusted linear regression model, protein intake was inversely associated with the EBIA (p = 0.005). The results suggest that family food insecurity jeopardizes the quality of children's diet, reducing the consumption of protein and increasing the consumption of coffee and high energy density foods.