The uncontrolled distribution of genetically modified organisms (GMO)-based food and feed is an increasing global concern, primarily due to limited information about their potential harmful effects. The growing diversity and complexity of GMOs present significant challenges for their detection, traceability, and safety monitoring. Traditionally, GMOs are detected using molecular methods, among which PCR methods are the most explored and are considered the gold standard. However, isothermal nucleic acid amplification methods, though less explored, hold great potential, especially when integrated with biosensor platforms, enabling the development of highly efficient and versatile biosensing systems. This paper provides a comprehensive overview of the recent advances in biosensors utilizing methods of isothermal nucleic acid amplification, highlighting their current progress and future perspectives. We discuss molecular methods for GMO detection, focusing on reaction conditions, amplification efficiency, and compatibility with various detection modalities. Additionally, we investigate the integration of various nanomaterials into transducers, such as electrochemical platforms, together with the electrochemical techniques and detection mechanisms, aiming to outline their synergistic effects with molecular techniques to improve detection sensitivity and enable real-time monitoring. Furthermore, we discuss the applications of GMO biosensors across diverse fields, including food safety and environmental monitoring, while addressing existing challenges and potential strategies for improving the performance, robustness, and practicality of biosensing platforms. Overall, this review highlights the significant progress achieved in GMO biosensors and underscores their promising role in advancing diagnostic and monitoring capabilities.