A method for managing the configuration of a host adapter is provided. The method provides for the access and configuration of a host adapter from within the computer operating system. Icons and graphical user interfaces are displayed providing a plurality of configuration options and diagnostic tools to allow access, evaluation, management and testing of host adapters and peripheral devices connected thereto in a manner with the look and feel of any other computer system device. When configuration changes are input, the method provides a prompt indicating the system must be rebooted for the changes to be implemented, and a reboot command for the user to execute. While executing the reboot command, the system flashes the host adapter configuration changes to the EEPROM on the host adapter, and the system initializes in accordance with the changed configuration settings. In addition to the method for managing the host adapter and associated configuration, also provided is the computer readable media with program instructions implementing the method.