Deployment of reconfigurable hardware or field programmable gate arrays (FPGAs) in cloud platforms is the modern trend. Practical scenarios include Amazon's EC2 F1 cloud services, Microsoft's Project Catapult and many others. Efficient task scheduling algorithms exist that can ensure green computing, i.e. order the operation of user tasks in the available FPGAs in such a manner that the power dissipated is optimum. But recent literature has exhibited eradication of the hardware root of trust, which is not taken into account by the existing task scheduling algorithms that can facilitate green computing. In this work, we analyze how vulnerability in hardware like hardware trojan horses (HTH) can increment power dissipation suddenly at runtime, without affecting the basic security primitives like integrity, confidentiality or availability of the system. Thus, are difficult to detect but may hamper the system due to unnecessary high power dissipation. We also develop a suitable runtime task scheduling algorithm which schedules the tasks at runtime based on the dynamic status of the resources, such that the power dissipation incurred at runtime is optimum. Finally, we also propose a mechanism via which we can detect affected cloud resources based on the runtime operations. We validate our proposed methodology via simulation based experiments. © 2020 IEEE.