Author summary: The regulation of genetically modified (GM) food products in several jurisdictions considers appropriate labelling to be a key requirement for food safety and to ensure the protection of consumer choices. In Nigeria, such regulations are enforced by relevant government agencies. There is, however, little information on compliance levels with appropriate labeling regimes of GM products in Nigeria. This study was conducted to ascertain compliance with existing labeling guidelines and regulations for GM food products sampled from Abuja, Nigeria. DNA-based real-time polymerase chain reaction detection procedures were used to evaluate 15 processed and semi-processed pre-packaged food products obtained from retail stores in Abuja for the presence of specific regulatory sequences specific to GM products. Three regions present in GM food products were targeted, namely, the 35S promoter gene from cauliflower mosaic virus and figwort mosaic virus, with the nopaline synthase terminator from Agrobacterium tumefaciens. Eleven out of the 15 samples showed positive amplification for at least one regulatory sequence signature unique to GMOs, out of which only two were appropriately labeled as required by regulation. While the safety of GM products is a prerequisite for commercialization, labelling is required to protect consumer preference. The roles of relevant government agencies in developing appropriate labeling guidelines and enforcing the same to protect consumers’ choices are discussed. This study successfully utilized qPCR-based methods, which is an incredibly sensitive and well-accepted method for GMO screening, to ascertain the prevalence of genetically modified products sold in local stores in Abuja, Nigeria.