An example method for transformation of Peripheral Component Interconnect Express (PCIe) compliant virtual devices in a server in a network environment is provided and includes receiving, during runtime of the server, a request to change a first configuration of a PCIe compliant virtual device to a different second configuration, identifying a bridge on a PCIe topology below which the virtual device is located, issuing a simulated secondary bus reset to the bridge, the virtual device being reconfigured according to the change in configuration after the simulated secondary bus reset is issued, re-enumerating below the bridge after the change in configuration completes without rebooting the server, and updating the PCI topology with the virtual device in the second configuration. A virtual interface card adapter traps the simulated secondary bus reset, removes the virtual device from the PCI topology, and reconfigures the virtual device from the first configuration to the second configuration.