The conventional computing techniques are based on the assumption of a near constant source of input power. While this assumption is reasonable for high-end devices such as servers and mobile phones, it does not always hold in embedded devices. An increasing number of Internet of Things (IoTs) is powered by intermittent power supplies which harvest energy from ambient resources, such as vibrations. While the energy harvesters provide energy autonomy, they introduce uncertainty in input power. Intermittent computing techniques were proposed as a coping mechanism to ensure forward progress even with frequent power loss. They utilize non-volatile memory to store a snapshot of the system state as a checkpoint. The conventional security mechanisms do not always hold in intermittent computing. This research takes a top-down approach to design secure intermittent systems. To that end, we identify security threats, design a secure intermittent system, optimize its performance, and evaluate our design using embedded benchmarks. First, we identify vulnerabilities that arise from checkpoints and demonstrates potential attacks that exploit the same. Then, we identify the minimum security requirements for protecting intermittent computing and propose a generic protocol to satisfy the same. We then propose different security levels to configure checkpoint security based on application needs. We realize configurable intermittent security to optimize our generic secure intermittent computing protocol to reduce the overhead of introducing security to intermittent computing. Finally, we study the role of application in intermittent computing and study the various factors that affect the forward progress of applications in secure intermittent systems. This research highlights that power loss is a threat vector even in embedded devices, establishes the foundation for security in intermittent computing. / Doctor of Philosophy / The embedded systems are present in every aspect of life. They are available in watches, mobile phones, tablets, servers, health aids, home security, and other everyday useful technology. To meet the demand for powering up a rising number of embedded devices, energy harvesters emerged as a solution to provide an autonomous solution to power on low-power devices. With energy autonomy, came energy scarcity that introduced intermittent computing, where embedded systems operate intermittently because of lack of constant input power. The intermittent systems store snapshots of their progress as checkpoints in non-volatile memory and restore the checkpoints to resume progress. On the whole, the intermittent system is an emerging area of research that is being deployed in critical locations such as bridge health monitoring. This research is focused on securing intermittent systems comprehensively. We perform a top-down analysis to identify threats, mitigate them, optimize the mitigation techniques, and evaluate the implementation to arrive at secure intermittent systems. We identify security vulnerabilities that arise from checkpoints to demonstrate the weakness in intermittent systems. To mitigate the identified vulnerabilities, we propose secure intermittent solutions to protect intermittent systems using a generic protocol. Based on the implementation of the generic protocol and its performance, we propose several optimizations based on the needs of the application to securing intermittent systems. And finally, we benchmark the security properties using two-way relation between security and application in intermittent systems. With this research, we create a foundation for designing secure intermittent systems.