The prevalence of micronutrient deficiencies and non-communicable diseases are on the rise in Sub-Saharan Africa (SSA) despite the abundance of indigenous nutritious and biofortified crops. Rapid urbanisation and poor dietary habits have resulted in most Ghanaian households frequently consuming highly processed foods, sugar, salt, and unhealthy fats in place of complex carbohydrates such as whole grains, root and tuber crops, fruits, and vegetables. Existing postharvest and food processing practices may also not help consumers to make healthy food choices that would result in optimal nutrition. Applying a food systems approach will enable stakeholders to consider the solutions to these public health concerns through different lenses along the agricultural value chain. This review examines nutritious indigenous crops in Ghana, that include millet, sorghum, soybean, locust bean, aerial yam, taro, and cocoyam, considering how their nutrient composition could aid in disease prevention and health promotion among the populace. In addition, biofortified crops such as yellow and orange maize, high iron bean, yellow cassava, and orange-fleshed sweetpotato are discussed, highlighting the focal nutrients and their relation to health improvement. This review employs the food systems approach to critically examine how nutrition can be maximised along the various steps of the agricultural value chain. It concludes with recommendations at the individual and policy levels that could result in medium- and long-term positive impacts on nutrition and health status.