A hot-plugged PCIe device configuration system includes a PCIe device with a PCIe configuration space having PCIe configuration space registers. A computing system includes a PCIe connector and a PCIe setting record database storing a first PCIe setting record having a first register write location value and first register value information. The computing system detects that the PCIe device has been hot-plugged into the PCIe connector, and uses the first register write location value in the first PCIe setting record to determine a location in the PCIe configuration space that provides a first PCIe configuration space register. The computing system then uses the first register value information in the first PCIe setting record to determine at least one register value change for the first PCIe configuration register, and writes the at least one register value change to the first PCIe configuration space register using the location.