Background Genome editing by CRISPR/Cas9 has become a popular approach to induce targeted mutations for crop trait improvement. Soybean is an economically important crop worldwide. Gene editing has been demonstrated in soybean. However, its utilization in stably transformed plants through whole plant regeneration is still not widespread. The study aims to establish a simple and efficient system that transmits the mutations and altered traits to progenies. It specifically will utilize CRISPR/Cas9-mediated mutagenesis in stably transformed soybean. Methods Researchers selected soybean phytoene desaturase genes or P-D-S (PDS) for editing through nonhomologous end joining. Three constructs targeting PDS gene specifically. Additionally, two constructs targeting both genes simultaneously, using one guide RNA in each construct, was made. Agrobacterium-mediated transformation of cv. Williams 82 using half-seed explants dissected directly from overnight-imbibed seeds was performed. Mutations at desired loci were induced in T0 plants, and were transmitted to T1 progenies. Key findings Simultaneous targeting of both PDS genes resulted in visible mutant phenotypes in both T0 and T1 generations. Deletion was the predominant mutation type, although 1-nucleotide insertion was also observed. Modifications in both PDS genes were transmitted to T1 progenies. Strong mutant phenotypes were also observed in T1 plants. Conclusion Using simple constructs containing one guide RNA demonstrated efficient CRISPR/Cas9-mediated mutagenesis in stably transformed soybean plants. This showed that mutations could be inherited in progenies. The established system can be employed to edit other genes in soybean through whole plant transformation. This can be done in a bid to achieve agronomic trait improvement.