Objectives  Non-communicable diseases (NCDs) and childhood obesity are increasing in sub-Saharan Africa. To prevent childhood obesity in Malawi, it is necessary to understand the factors affecting food choices in the population. We examined the factors influencing food choices that may affect childhood obesity from their mothers’ perspective.Methods  We conducted focus group interviews with mothers with children aged 2-4.9 years in Lilongwe City (as an urban area) and Mzimba District (as a rural area). Data were analyzed thematically using NVivo software.Results  The sample for this analysis included 43 mothers. A wide variety of foods were present in the two regions in the study area. Factors influencing food choices were extracted as; financial limitations; and seasonal effects. Children are fed the same food as their mothers, including carbonated drinks, but they are also given a special diet for children, which consists of porridge with soya flour, milk, and margarine. Eggs and pork were socially and culturally identified as foods not given to mothers during pregnancy, whereas children are given eggs in some cases these days. Mothers identified; hygienic food, clothing and shelter; nutritious meals with good hygiene; and regular sustainable physical activity as essential for good health. Two themes were then identified as healthy diet; eating foods from a diverse range of food groups; energizing the body, preventing disease and promoting health. Mothers give carbonated drinks and juices to their children despite understanding that they are not good for them, while economic circumstances make it difficult for them to access foods from the six food groups that they know they should give to their children.Conclusion  It was suggested that “financial reasons” and “no enough intervention to reflect knowledge into practice” may have affected food choices and led to childhood obesity. Therefore, this study recommends that nutrition education for individuals and caregivers and health promotion initiatives based on a public health vision through price adequacy and access to healthy, nutritious, safe, affordable and easy-to-prepare foods should be encouraged as a preventive measure for childhood obesity.