Cyber-physical systems (CPS) integrate cyber-infrastructure comprising computers and networks with physical processes. The cyber components monitor, control, and coordinate the physical processes typically via actuators. As CPS are characterized by reliability, availability, and performance, they are expected to have a tremendous impact not only on industrial systems but also in our daily lives. We have started to witness the emergence of cloud-based CPS. However, cloud systems are prone to stochastic conditions that may lead to quality of service degradation. In this paper, we propose M2CPA - a novel framework for multi-virtualization, and multi-cloud monitoring in cloud-based cyber-physical systems. M2CPA monitors the performance of application components running inside multiple virtualization platforms deployed on multiple clouds. M2CPA is validated through extensive experimental analysis using a real testbed comprising multiple public clouds and multi-virtualization technologies.