Background: Reliable and efficient methods for detecting genetically modified organisms (GMOs) in unprocessed and processed food will be essential for establishing an effective system for traceability all along the supply chain. It is important to understand the detection of GMOs following microwave treatment, which is a common processing method used in various food products such as flours. Therefore, this study aimed to detect the presence of Cauliflower mosaic virus (CaMV) 35S promoter (P-35S), Figwort mosaic virus (FMV) promoter (P-FMV), and T-NOS (nopaline synthase terminator) genetic elements in DNA samples from untreated and microwave-treated genetically modified (GM) cereal flour samples using the qualitative polymerase chain reaction (PCR) based screening method.Please confirm if the author names are presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [Begüm Zeynep] Last name [Hançerlioğulları]. Also, kindly confirm the details in the metadata are correct. The author names were presented accurately and in the correct sequence (given name, middle name/initial, family name). Author 1 Given name: [Begüm Zeynep] Last name [Hançerlioğulları]. Author 2 Given name: [Remziye] Last name [Yılmaz]. The details in the metadata are correct. Methods and results: DNA was extracted from all samples, and the efficiency of the qualitative PCR screening technique was tested by the verification studies. We performed an inhibition study with plant-specific actin (ACT) gene to the effectiveness of confirming the DNA extraction method. Then, we made the confirming of the qualitative PCR system by method performance testing criteria. The high quality and quantity of the DNA extracts from untreated and microwave-treated flour samples indicated the applicability of qualitative PCR screening assays. The results showed that microwave radiation does not significantly impact the genetic element screening in flour materials. Conclusion: Untreated and microwave-treated flour samples had amplifiable DNA for the simultaneous screening of three genetic elements. The qualitative screening tests conducted in this study produced dependable outcomes, thus, can be successfully used for monitoring in control laboratories.