The aim of this study was to develop a nutrient‐enhanced millet‐based composite flour incorporating skimmed milk powder and vegetables for children aged 6–59 months. Two processing methods were tested to optimize nutrient content and quality of millet‐based composite flour, namely germination for 0, 24 and 48 hr and roasting at 80, 100, and 140°C. The amount of ingredients in the formulation was determined using Nutri‐survey software. Germinating millet grains for 48 hr at room temperature significantly ( p < 0.05) increased protein content (9.3%–10.6%), protein digestibility (22.3%–65.5%), and total sugars (2.2%–5.5%), while phytate content (3.9–3.7 mg/g) decreased significantly ( p < 0.05). Roasting millet grains at 140°C significantly ( p < 0.05) increased the protein digestibility (22.3%–60.1%) and reduced protein (9.3%–7.8%), phytate (3.9–3.6 mg/g), and total sugar content (2.2%–1.9%). Germinating millet grains at room temperature for 48 hr resulted in millet flour with the best nutritional quality and was adopted for the production of millet‐based composite flour. Addition of vegetables and skimmed milk powder to germinated millet flour significantly ( p < 0.05) increased the macro‐ and micronutrient contents and the functional properties of millet‐based composite flour. The study demonstrated that the use of skimmed milk powder and vegetables greatly improves the protein quality and micronutrient profile of millet‐based complementary foods. The product has the potential to make a significant contribution to the improvement of nutrition of children in developing countries.