Soybean has been grown as an important protein and oil crop for thousands of years. Additionally, it also has a high content of iso-flavonoids, folic acid and saponins, exhibiting various biological activities. It contains several antioxidants, and has anti-diabetic, anti-proliferative, anti-obesity and anti-inflammatory properties. However, soybean also contains various antinutritional factors such as trypsin inhibitor, agglutinin, lectins, phytic acid and tannins, which reduce nutrient utilisation. Attempts have been made to improve the nutritional quality of soybean through conventional breeding, but anticipated outcomes could not be met and these efforts primarily resulted in agronomically undesirable traits. However, the development of cutting-edge tools and technologies including high throughput genotyping, phenotyping, DNA sequencing techniques and genome editing have made great progress in improving the functional and nutritional qualities of soybean.