To evaluate DNA fragmentation and GMO quantification during soybean protein concentrate and isolate preparation, genetically modified soybean event GTS 40-3-2 (RRS) was blended with conventional soybeans at mass percentages of 0.9%, 2%, 3%, 5%, and 10%. Qualitative PCR and real-time PCR were used to monitor the taxon-specific lectin and exogenous cp4 epsps target levels in all of the main products and by-products, which has practical significance for RRS labelling threshold and traceability. Along the preparation chain, the majority of DNA was distributed in main products, and the DNA degradation was noticed. From a holistic perspective, the lectin target degraded more than cp4 epsps target during both of the two soybean proteins preparations. Therefore, the transgenic contents in the final protein products were higher than the actual mass percentages of RRS in raw materials. Our results are beneficial to the improvement of GMO labelling legislation and the protection of consumer rights.