A majority of households in Sub-Saharan Africa utilize cereal-based flours in the preparation of most of their staples. However, the micronutrient contents of these cereal-based flours are low with higher levels of anti-nutrients. Food to food fortification is being used as an alternative to improve the micronutrient content of the cereal-based flours. This study sought to develop an extruded composite flour using sorghum and maize as the cereal base and baobab, grain amaranth and orange-fleshed sweet potatoes as the fortificants. A completely randomized design in factorial arrangement with ingredient ratio and extrusion as factors and seven levels was used to develop different formulations of the composites. Fortification of sorghum-maize cereal flour blends with amaranth, baobab and orange-fleshed sweet potato powder resulted in a significant (p<0.05) increase in the protein, beta-carotene, iron and zinc contents, on average, 8.99 ±1.03 g/100g, 895.90 ±346.85 mg/100g, 11.81 ± 9.73 mg/100g and 1.74 ± 0.18 mg/100g dry weight basis respectively. High grain amaranth levels in the formulations significantly (p<0.05) increased the phytate content whereas tannin content was significantly lower in low sorghum formulations. Conversely, extrusion of the composite flours significantly (p<0.05) reduced protein and beta-carotene contents by 4.7% and 40.9% respectively. Extrusion and its interaction with ingredient ratio significantly (p<0.05) affected the proximate, mineral and anti-nutrient composition of the composite flours. Both the fortificants and extrusion play a role in the reduction of anti-nutrients and therefore future studies should focus on other treatments that can be used together with extrusion to reduce anti-nutrients.