A system and method are disclosed for a flexible routing engine in a PCIe switch. The system may include a switch manager that is enabled, through firmware, to configure one or more routing tables associated with a switch stack of a PCIe switch. To enable non-transparent bridging and non-standard routing, the method may include receiving a transaction layer packet at a translated routing port of a PCIe switch, and performing translation of the address and requester ID of the packet utilizing tables that are updated by the firmware of the switch manager to route the packet through the switch.