A hybrid cloud computing system is managed by determining communication affinity between a cluster of virtual machines, where one virtual machine in the cluster executes in a virtualized computing system, and another virtual machine in the cluster executes in a cloud computing environment, and where the virtualized computing system is managed by a tenant that accesses the cloud computing environment. After determining a target location in the hybrid cloud computing system to host the cluster of virtual machines based on the determined communication affinity, at least one of the cluster of virtual machines is migrated to the target location.