A computing system peripheral device compatible with the peripheral component interconnect express (PCI-E) protocol responds to a DL_DOWN command primitive by configuring a general-purpose input/output (GPIO) port into a known state without invoking a GPIO module reset. In addition, select resources are excluded from resources on the peripheral device that are issued a reset command. The select resources can include a GPIO module, a memory element and a PCI-E SERDES module. After the remaining reset resources have completed their individual initialization processes, the central processor core on the peripheral device is reset. The described response to the DL_DOWN command primitive avoids cache data loss, masks signal transitions on I/O ports and timing problems that prevent some peripheral devices from being recognized in a computer's basic input/output system (BIOS).