A method and a computer readable medium comprising instructions for upgrading a firmware of a peripheral device connected to a host device via a Peripheral Component Interconnect Express (PCIe) bus from the operating system (OS) of the host device is disclosed. In one embodiment, the method and computer readable medium instructions includes halting host device access to the peripheral device after detecting the peripheral device has completed a shutdown sequence, and resetting the peripheral device after a predetermined time period after completion of the shutdown sequence. The method and computer readable medium instructions further includes initializing the firmware stored in a persistent storage location of the peripheral device, and re-establishing a connection between the peripheral device and the host device. In one embodiment, the predetermined time period is greater than a time it takes for the host device to detect the peripheral device has completed the shutdown sequence. In one embodiment, the peripheral device is a Non-Volatile Memory Express (NVMe)-compliant data storage device.