A method of remediating system services relies on a first dependency graph with super nodes, to each of which a set of system services are assigned, and second dependency graphs, each of which represents dependencies among the system services that are in one of the sets. The method includes the steps of: comparing an actual configuration state of the system services to a desired configuration state of the system services to identify configurations that are in drift; identifying system services corresponding to the configurations that are in drift; determining an order of updating configurations of the identified system services using the first and second dependency graphs; and applying the desired configurations of the identified system services in the order determined, wherein after the configurations of an identified system service are updated, the system service executes with the updated configurations.