Technologies for secure certificate management include a computing device that receives a keystore command related to an encryption key, converts the keystore command into an encrypted database command, unlocks an encrypted database stored by the computing device with an obfuscated passphrase, and executes the encrypted database command. The encrypted database includes a key table to store binary copies of encryption keys and a metadata table to store metadata related to the encryption keys. The computing device returns a response to the keystore command in response to executing the encrypted database command. The keystore command may be received and the response may be returned via a command-line interface or a machine-to-machine interface. The computing device may load multiple encoded passphrase segments from corresponding predetermined file system locations, decode the encoded passphrase segments, and compound the decoded passphrase segments to generate the passphrase. Other embodiments are described and claimed.