Pulse crops have been an essential component of South Asian food habits and a major source of protein for the vegan population. The global production of pulses has increased significantly with the pulses revolution in India, which shares 24–25% of it. From 82.56 million tons in 2014, global pulses production recorded an all-time high in 2017 with 98.72 million tons (a 19.56% increase) and restored to 96.83 million tons in 2018 (17.28% increase). Likewise, in India, the pulses production increased from 17.15 million tons in 2014–15 to 26.05 million tons in 2022–23. Genetic enhancement and breeding for nutritional and grain quality is going to be a major avenue of research after the considerable achievement in production increase of pulse crops. Breeding for nutritional and grain quality in pulse crops needs wide-scale screening of genotypes with high-throughput phenotyping protocols to identify the trait-specific donors for their utilization in hybridization program. Early generation selection of seed-based traits being an issue, selection strategies need to be worked out. Rapid generation advancement and attainment of homozygosity may help to address this issue of phenotyping the segregating generation and selection. Policy support in the form of setting relevant criteria for nutritionally superior or biofortified genotypes in the variety release system and ensuring premium price to the growers to maximize their returns are essential. Considerable research progress has been made for protein content enhancement in chickpea and pigeonpea relating to identification of the high-protein donors, working out the inheritance pattern, and genetic mapping. Nutrition profiles of the major pulse crops have been studied by the conventional biochemists; this information will be the initial benchmark for the genetic enhancement programs. Traits like the concentration of beta-carotene, Fe, Zn, folate, etc., in seeds, along with grain quality traits, have been studied in different pulse crops. High-throughput nondestructive phenotyping protocol and selection strategies for handling segregating generation are major bottlenecks for breeding for nutritional or grain quality in pulse crops. Nutritional and grain quality breeding for pulses is an interdisciplinary approach involving the plant breeders, biochemists, processing engineers, and food technologists; a holistic approach is needed to address the nutritional security issue through this approach.