Embodiments are described for executing embedded functions in endpoint devices by proxy in a shared PCI Express subsystem. The shared subsystem comprises a plurality of proxy devices coupled to a PCIe fabric, wherein each one of the proxy devices is associated with an endpoint device and coupled to a controlling server through a PCIe link. An associated proxy device comprises a copy of the configuration space of the target endpoint device. Embedded functions of an endpoint device can be accessed by controlling servers through the associated proxy devices. Devices in the shared subsystem use PCI protocol to communicate. The duplication of the endpoint configuration space in the proxy device is administrated by a proxy configuration manager. The proxy device translates destination addresses in upstream and downstream transactions. A proxy interrupt conveyance mechanism relays interrupt messages from an endpoint device to the controlling server via the associated proxy device.