Mineral fertilization is considered to be useful for improving soil fertility and yields. However, its use is linked to global warming and soil and water pollution by its rapid mobilization. On the other hand, organic fertilization is recommended to maintain or improve soil organic carbon and total nitrogen stocks while contributing to climate change mitigation. The main goal of this study was to assess the effect of two different fertilizer types, mineral and organic, during three cowpea crop cycles on the soil’s physicochemical properties, enzyme activities, crop yield, crop quality and nutritional composition when considering two cowpea cultivars (Feijão frade de fio preto (FP) and Feijão frade de fio claro (FC)). The use of mineral fertilizers was seen to contribute to improved soil fertility due to the increase in soil properties, such as recalcitrant carbon, total nitrogen, ammonium content, available K and available Mg. On the other hand, organic fertilizers only increased the nitrate content in the soil. There were no differences in terms of cowpea crop yield, quality and nutritional composition by fertilizer type. Thus, both fertilizer types contributed to the same crop yield and quality, and thus the use of organic fertilizers can result in a sustainable alternative for maintaining cowpea crop yield and quality.