An in-band protocol transport carries command-response protocol communications between first and second functional components of a storage input/output (I/O) interface stack, for example to control encryption-related processing of storage I/O commands. A storage read command used as a protocol transport message has protocol data in a read data buffer, and predetermined read address information, such as a prime-numbered starting block address and a small, odd-valued length value, unlikely to occur in normal (non-transport) storage read commands. The second functional component determines that the storage read command contains the predetermined read address information, indicating that the storage read command is a protocol transport message rather than a normal read. For greater confidence, it also determines that the protocol data in the read data buffer includes protocol identification data such as a protocol signature. The protocol data is used to control a processing action for subsequent normal storage I/O commands, such as encryption-related processing, and a protocol response is returned by creating and storing response data in the read data buffer and signaling completion of the storage read command to the first functional component.