Methods and systems for managing reset of a physical function of an I/O device in a computing system are disclosed, where the physical function is included in a single-root PCI manager. One method includes maintaining a count of active virtual functions associated with the physical function included in the single-root PCI manager, and, upon determining that no active virtual functions are associated with the physical function, allowing the physical function to be reset within the single-root PCI manager. The method further includes while resetting the physical function, persisting a configuration memory space associated with the physical function, and associating the persisted configuration memory space with the physical function after the physical function is reset.