Soybean is the most cultivated GM crop worldwide, being planted on 47% of the global GM crop area. However, GM crops have not been widely publicly accepted. Thus, countries have established regulations for the labeling of GM foods to inform consumer decision making. In 2010, regulations on GM foods began to be enforced in Turkey. To meet these legislation requirements, the development of reliable detection methods is an important priority in this research area. PCR-based methods are most commonly used for this purpose. However, processing factors (low pH, heat etc.) affect DNA quality and thus the sensitivity of PCR. The aim of this study was to evaluate the combined effects of heat and pH on the detection of GM soy in meat products. We found that the combined effects of heat and low pH affect the detection limit, but low levels of GM soy can still be detected after processing.