Security and vulnerability mitigation are critical imperatives in the dynamic landscape of the Internet of Things (IoT). This article delves into risk management and cybersecurity in IoT systems, with an emphasis on Field-Programmable Gate Array (FPGA) devices. This underscores the need to assess threats, vulnerabilities, attacks, and compromises in both the design and operation of these systems, showing a process to mitigate IoT threats. FPGA devices, which are recognized for their flexibility and adaptability, have emerged as essential elements for safeguarding security in the physical layer of IoT systems. The protection of FPGA devices against electrical overloads and transients was examined in detail, highlighting the urgency of implementing detection and mitigation mechanisms for denial-of-service attacks. Performance testing is addressed by implementing two countermeasures against IoT threats as a crucial element for evaluating the robustness and reliability of these devices in IoT environments, while emphasizing the need to comply with recognized security standards.