In Brazil, although many children from low income families attend day care centers with appropriate hygiene practices and food programs, they have nutritional disorders and communicable diseases. This quantitative and qualitative cross-sectional study identified staff challenges in child day care centers and suggested alternative activity management to prevent nutritional disorders and communicable diseases. The study included 71 nursery teachers and 270 children from public and philanthropic day care centers (teacher to child ratios of 1:2.57 and 1:6.40, respectively). Interviews and focus groups were conducted with teachers and parents, and anthropometry and blood samples were drawn from the children by digital puncture. Children in philanthropic child day care centers were more likely to be hospitalized due to communicable diseases. Teachers from philanthropic child day care centers had lower age, income and education and higher work responsibilities based on the number of children and working time. The focus groups characterized institutions with organized routines, standard food practices, difficulties with caretaking, and lack of training to provide healthcare to children. Strategies to improve children’s health in day care settings should focus on training of teachers about healthcare and nutrition.