The selection of superior cultivars through the combination of high yield and protein content cowpea seeds in semi-arid tropical regions have a huge positive impact on the production-market chains in places where there is short availability of protein sources for human consumption. The main aim of the present study is to estimate the adaptability and stability parameters of total seed yield and protein content in cowpea genotypes in order to release new cultivars by combining these value-added traits. Forty-four inbred lines and cultivars were assessed under seven different environmental conditions, either rain-fed or irrigated crop management, in seven sites the Brazilian semi-arid region. The seed protein content was quantified through the Kjeldahl method. Grain yield was adjusted in mean of plant per plot by the covariance method. Statistically significant differences in the genotype as well as in the genotype×environment interaction were observed in all the assays. The inbred lines presenting the highest protein contents showed the lowest grain yields, and it indicated the prominent “phenotypic cost” of protein in overall cowpea seed production. However, the breakage between the herein assessed association was observed in inbred lines subgroups such as ‘C3Q’, ‘C3M’, ‘C2S’, and ‘CIJ’. These lines showed yield close to or above 1050 kg/ha and mean protein content of 27%, as well as good adaptability and stability in different environments, as it was simultaneously indicated through two methodologies. Therefore, these inbred lines may represent a potential elite germplasm in cowpea breeding programs and/or in the releasing of new cultivars adapted to the semi-arid region.