To evaluate DNA fragmentation and GMO quantification during soya bean protein concentrate and isolate preparation, genetically modified soya bean event GTS 40-3-2 (Roundup Ready
TM
soya bean, RRS) was blended with conventional soya beans 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 soya bean 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.