A system and method for dynamic reconfiguration of at least one peripheral bus switch of a system includes a management controller that detects whether a server system is connected to each peripheral bus slot of the system. The management controller selects a peripheral bus switch topology for the at least one peripheral bus switch, based on the detecting. The management controller sets each port of the at least one peripheral bus switch to either an upstream port configuration or a downstream port configuration, based on the peripheral bus switch topology.