A method of remediating configurations of a plurality of system services running in each of a plurality of hosts, wherein each of the hosts is configured with a virtualization software for supporting execution of virtual machines therein, includes the steps of: retrieving actual configurations of the system services, wherein the actual configurations are stored in accordance with a configuration schema of the system services and include a user configuration, which is a configuration initiated by the user, and a system configuration, which is a configuration initiated by the host in response to the user configuration; retrieving desired configurations of the system services from a desired configuration file; comparing each of the actual configurations with a corresponding one of the desired configurations; and upon determining that at least one actual configuration, which is not a system configuration, is different from a corresponding one of the desired configurations, replacing the at least one actual configuration with the corresponding desired configuration.