Soybean is an excellent source of high quality protein and vegetable oil for human and animals. The diverse and increasing demands for soybean have created enough opportunities for breeders to improve the soybean seed composition traits influencing nutritional parameters. Protein and oil content, protein subunit composition, fatty acid composition, anti-nutritional factors etc. are some of the important seed traits that need to be improved to enhance the nutritional value of soybean as food and feed. Many studies have been carried out to modify the seed composition traits to enhance the nutritional quality of soybean. The extensive screening of worldwide soybean germplasm collections has led to the identification of many genotypes with significant variation for seed composition traits. In addition, induced mutagenesis has contributed immensely in improving the quality of soybean seeds by creating novel mutant genotypes for various seed quality traits. Gene/QTL mapping and molecular characterization of these mutants had led to elucidation of gene function and significantly increased the knowledge on molecular basis of seed composition traits. The emergence of modern biotechnological tools like siRNA and targeted mutagenesis techniques like CRISPR/Cas9 has further opened new opportunities in modifying the nutritional value of soybean. This review article provides comprehensive and up-to-date knowledge about the genetic improvement of important seed composition traits in soybean by conventional and biotechnological approaches. The article also discusses the major challenges and limitations in genetic enhancement and utilization of quality related traits in soybean.