Protecting configuration data in a clustered container system may include, in some embodiments, protecting an ETCD data store in a Kubernetes cluster. A data storage management system addresses the unique needs of protecting an ETCD data store of a target Kubernetes cluster, as well as protecting non-ETCD data payloads. The illustrative data storage management system defines ETCD as a unique kind of workload. ETCD protection is integrated within the data storage management system, which automatically creates data structures and resources within the system for, and provides special-purpose features to protect, ETCD contents and associated security certificates. One of the special-purpose features deploys a temporary data transfer agent within the target Kubernetes cluster to safeguard an ETCD snapshot and transmit its contents, along with the security certificates, to a backup infrastructure that operates outside of the target Kubernetes cluster. The backup infrastructure comprises components deployed by the data storage management system.