A data processing system includes an input/output (I/O) host bridge to which at least one I/O adapter is coupled by an I/O link. In a register of the I/O host bridge, a configuration partitionable endpoint (PE) field is set to identify a PE to be used for an I/O configuration operation. Thereafter, the host bridge initiates the I/O configuration operation on the I/O link and determines if an error occurred for the I/O configuration operation. In response to a determination that an error occurred for the I/O configuration operation, an error state is set in the I/O host bridge only for the PE indicated in the configuration PE field of the register in the I/O host bridge, wherein I/O configuration errors are isolated to particular PEs.