A method and data processing system enables scheduling of atomic operations within a Peripheral Component Interconnect Express (PCIe) architecture during page migration. In at least one embodiment, firmware detects the activation of a page migration operation. The firmware notifies the I/O host bridge, which responds by setting an atomic operation stall (AOS) bit to a pre-established value that indicates that there is an ongoing migration within the memory subsystem of a memory page that is mapped to that I/O host bridge. When the AOS bit is set to the pre-established value, the I/O host bridge prevents/stalls any received atomic operations from completing. The I/O host bridge responds to receipt of receipt of an atomic operation by preventing the atomic operation from being initiated within the memory subsystem, when the AOS bit is set to the pre-established value. The AOS bit is reset when the migration operation has completed.