An embedded port of a host bus adapter of a storage controller receives, from a driver of the host bus adapter, a first set of commands to quiesce I/O operations in the embedded port for a first period, wherein hardware resets of buses and other logic to which the embedded port is connected are performed in the first period of quiescing of I/O operations. One or more commands are received to resume selected I/O operations in the embedded port. A second set of commands is received to quiesce I/O operations for a second period. A command is received to allow normal I/O operations, subsequent to the driver being reinitialized during the second period of quiescing of I/O operations.