Reconfigurable computing is becoming ubiquitous in the form of consumer-based Internet of Things (IoT) devices. Reconfigurable computing architectures have found their place in safety-critical infrastructures such as the automotive industry. As the target architecture evolves, it also needs to be updated remotely on the target platform. This process is susceptible to remote hijacking, where the attacker can maliciously update the reconfigurable hardware target with tainted hardware configuration. This paper proposes an architecture of establishing Root of Trust at the hardware level using cryptographic co-processors and Trusted Platform Modules (TPMs) and enable over the air updates. The proposed framework implements secure boot protocol on Xilinx based FPGAs. The project demonstrates the configuration of the bitstream, boot process integration with TPM and secure over-the-air updates for the hardware reconfiguration.