Key manager systems and methods for a QKD-based network are disclosed. The system includes a QKD layer that generates quantum encryption keys, a persistent storage layer that stores the quantum encryption keys, and a key management layer. The key management layer generates an application registration record that includes a list of multiple applications that use the quantum encryption keys. The key management layer also generates a corresponding key storage layer. The multiple applications reside in an applications layer. The applications in each node remove keys from the key storage layer so that each node can encrypt/decrypt data using quantum encryption keys. The methods also include secure QKD system boot-up and authentication that facilitate implementing a commercial QKD system in real-world environments.