The selection and development of adaptable cultivars for specific conditions is the first step in implementing cultivation practices to ensure stable, high-quality vegetables with superior nutritional value. Traditional breeding methods are based on strategies such as selective breeding, mass selection, pure-line selection, backcross, and hybrid breeding, the latter taking advantage of heterosis effects. Advanced techniques such as phenomics, molecular markers, genome-wide association studies, and next-generation sequencing facilitate identifying and selecting desirable traits, enhancing nutritional quality. Biotechnological approaches, including gene transfer methods and CRISPR/Cas9, can improve vegetable quality by introducing specific genes. This review covers classical, advanced, and modern breeding strategies for improving nutritional quality in fruit and leaf vegetables under protected cultivation, focusing on genetic modifications to enhance pigments, vitamins, and minerals and reduce anti-nutritional characteristics. Techniques such as transgenic approaches and CRISPR/ Cas9 are utilized to develop zeaxanthin-rich tomatoes and enhance beta-carotene content in eggplants. Additionally, the review highlights specific nutritional traits in individual vegetables, such as bitterness in cucumbers, browning in eggplants, and mineral content in lettuce. Improving nutritional quality requires adaptive breeding across diverse conditions to produce stable varieties.