Protein and minerals are essential for human health, yet deficiencies persist worldwide. This study aimed to evaluate the genetic variability and heritability of protein and mineral contents in cowpea (Vigna unguiculata L. Walp) through a full-diallel hybridization experiment involving five dwarf cowpea cultivars. The experiment was conducted under controlled greenhouse conditions, assessing protein content (PC) and key mineral concentrations, including phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), manganese (Mn), sulfur (S), iron (Fe), copper (Cu), and zinc (Zn), in both parental lines and their hybrids. The variance analysis results indicate significant genetic variability (p < 0.01) among the cowpea genotypes for PC and mineral composition. The highest PC was observed in the “Ülkem × Amazon” and “Ülkem × Karagöz” hybrids (24.45%), indicating their potential for breeding high-protein cowpea lines. In terms of mineral composition, the “Karagöz × Amazon” hybrid exhibited the highest manganese content (34.69 ppm), while the “Sırma × Karagöz” hybrid had the highest iron content (33.06 ppm). The Karagöz parent line demonstrated superiority in zinc accumulation (34.75 ppm), making it a promising candidate for biofortification. Conversely, the “Sırma × Amazon” hybrid displayed the lowest protein (20.69%) and generally lower mineral values, indicating limited utility in breeding programs. Overall, the genotypes Ülkem and Karagöz emerged as the most promising parental lines for improving protein and mineral content in cowpea breeding efforts. General combining ability (GCA) and specific combining ability (SCA) analyses highlighted cultivars Ülkem and Karagöz as promising candidates for breeding programs. Notably, the hybrid “Karagöz × Amazon” exhibited high Mn (34.69 ppm), while “Ülkem × Karagöz” had the highest PC (24.45%). Broad-sense heritability estimates were highest for PC and Zn (0.99 and 0.64, respectively), suggesting a strong genetic influence on these traits. In conclusion, these findings provide useful guidance for enhancing cowpea’s nutritional profile through selective breeding.