This study aimed to develop high-quality flatbreads for low-income countries by using composite flours from climate-resilient crops, i.e., sprouted sorghum, tapioca, and cowpea, as partial alternatives to imported wheat. Through the experimental design, several flatbread prototypes were developed that maximized the content of sprouted sorghum and cowpea flours and minimized the content of wholewheat flour. Three of them were chosen based on the best textural, nutritional (highest intake of energy, proteins, and micronutrients—iron, zinc and vitamin A), and economic (cheapest in Sierra Leone, Tanzania, Burundi, and Togo) features. The physicochemical properties, in vitro starch digestibility, total phenolic content, antioxidant capacity, and sensory acceptability were also measured for the samples. The experimental flatbreads showed lower rapidly digestible starch and higher resistant starch contents than the control (100% wholewheat based), and were also richer in phenolic content and higher in antioxidant activity. Moreover, one of the prototypes was perceived to be as acceptable as the control for texture and flavour properties. The ranking test, performed after explaining the nature of the samples, revealed that the flatbread meeting the nutritional criteria was the preferred one. Overall, the use of composite flour from climate-resilient crops was proven to be an efficient strategy to obtain high-quality flatbread.