Methods and apparatus for enhancing control-plane security of a network-accessible service are described. In accordance with a security policy, one or more control servers are selected to perform administrative operations associated with configuration of a service instance at a particular instance host of a network-accessible service. The control servers may differ in security properties from the instance host. In response to a configuration request directed at the instance host, administrative operations are implemented at the selected control servers. A low-level command is issued for execution to the instance host from a control server. A result of the low-level command is obtained at the control server and is used to determine a response to the configuration request.