<p>Pigeonpea (<i>Cajanus cajan</i> L. Millsp.), South Asia’s second most significant pulse crop and source of dietary protein, is facing production issues due to a lack of improved varieties with high nutritional and seed quality compositions, as well as environmental stress. Identification of genes/alleles governing the nutritional and seed quality traits is key for marker-assisted breeding for quality traits in pigeonpea. Hence, the present study was undertaken to unravel the complex genetic architecture of nutritional and seed quality traits in pigeonpea. We conducted a genome-wide association study (GWAS) to identify SNP markers associated with nutritional traits, namely total protein content (TPC), phenolics content, and seed quality traits, such as seed coat colour, length, width, size, shape, and weight using a 62K SNP genotyping chip array. We estimated TPC of a panel of 287 diverse pigeonpea genotypes using Kjeldahl method to identify 5 significant SNPs associated with TPC on chromosomes 6 and 11 (AX-165344137), encoding a putative disease resistance protein, and Chromosome 11 (AX-165358192), encoding a CBL-interacting serine/threonine-protein kinase. We identified five markers associated with the seed coat colour on Chromosomes 5 (AX-165369586), 2 (AX-165370277), and 8 (AX-165400346). Additionally, we identified 4, 6, 2, 3, 6, and 5 SNPs associated with phenolics content, seed length, seed shape, seed width, seed size, and seed weight, respectively. The study’s findings are projected to bring considerable benefits to pigeonpea producers in marker-assisted breeding for the production of varieties with improved protein content and seed quality traits corresponded to consumer preferences, as well as promote improved health and nutrition. Therefore, GWAS provides strong support for exploring the genetic mechanisms underlying important pigeonpea qualities and improving breeding strategies.</p>