Methods and systems for upgrading an intelligent server adapter (ISA) with reduced downtime that affects performance are provided. The method includes, from a main agent, initiating a backup agent that includes critical functions of the ISA and runs in a tight loop, isolated from other components. The main agent transfers critical duties to the backup agent and shuts down before performing the upgrade. After upgrading itself and other system components, the main agent retrieves the duties from the backup agent, and may terminate the backup agent.