VLSI advancements have enabled proliferation in the Internet of Things(IoT) domain where small scale System-on-a-Chip (SoC) are employed as sensors or actuators. IoT devices are connected with other IoTs and with backend facilities. In today's world IoT is ubiquitous and pervasive, as system designers continue to use IoT based designs. In order to improve the lifespan of a device, hardware reconfigurability has security and functional applications for IoTs. Connectivity, while essential to the operation for an IoT device, also acts as a door for malicious actors. This work explores and identifies the threats to emerging IoT in the spaces of authentication, integrity, confidentiality and communication. For reconfigurable devices, the work extends boot time security and provides solution for Over the Air update mechanisms for reconfigurable architectures. This work uses automotive and smart grid to demonstrate applications of the research outcomes.