The modern aerial vehicle ecosystem relies heavily on various wireless communication and navigation technologies that are often unauthenticated and vulnerable to adversarial interference. This thesis evaluates the security of three critical components of automation systems in modern aerial vehicles: instrument landing system (ILS), aviation datalink applications like controller-pilot datalink communications (CPDLC), and satellite navigation systems such as global positioning system (GPS).First, we demonstrate the feasibility of manipulating ILS instruments using commercially available software-defined radio (SDR) and a closed-loop ILS spoofer capable of manipulating spoofing signals based on the aircraft's position. In the second part, we propose a spoof-and-jam strategy to manipulate flight crew decision-making by implementing a reactive jammer for aviation datalink applications with a fast reaction time and high jamming success rate. The third part investigates the feasibility of controlling unmanned aerial vehicle (UAV) movements solely by GPS spoofing, highlighting the challenges of achieving a complete UAV takeover without causing crashes. We explore generic and UAV-specific strategies to control the UAV's speed and direction, successfully taking over consumer-grade UAVs from leading manufacturers. Finally, to address security issues surrounding satellite navigation, we design and implement SemperFi, a single antenna GPS receiver capable of tracking legitimate GPS signals and autonomously recovering from spoofing attacks. Sem-perFi leverages the extended Kalman filter (EKF) sensor-fusion mechanism built into most existing UAVs and a custom-designed legitimate signal retriever module to recover from attacks with high accuracy and a fast recovery time.Overall, we address critical security concerns in modern aerial vehicles and pave the way for developing secure autonomous technologies by leveraging interconnected and tightly coupled sensors and individual systems.