Methods, systems, and products are disclosed for operating Peripheral Component Interconnect (`PCI`) Express resources in a logically partitioned computing system that include: allocating, by a hypervisor installed on the computing system, a PCI Express adapter installed in the computing system to a logical partition of the computing system, including establishing a data communication path between a processor of the computing system and the PCI Express adapter, the data communication path including a link between a PCI Express root complex and the PCI Express adapter; and administering, by the hypervisor for the logical partition, the PCI Express root complex and the link between the PCI Express root complex and the PCI Express adapter.