We demonstrate the manipulation of magnetic phases in FeRh thin films through atomic displacements and the distribution of structural defects. Atomic scale disorder can be controlled via irradiation with light noble gas ions, producing depth-varying nanoscale phase configurations of distinct antiferromagnetic, ferromagnetic, and paramagnetic regions. Here, we perform a spatial characterization of the magnetic phases and the local magnetic environment around the Fe atoms, as well as the variation of the open-volumes around atomic sites. Thus, a direct correspondence between the existence of the three magnetic phases and lattice defects is revealed. By careful selection of the irradiating fluence, we show that it is possible to produce simple and thermally stable magnetic configurations, such as uniform magnetization or a bilayer phase structure. Furthermore, the thin film surface and interfaces are observed as the nucleation sites for the transitions between the phases. These results demonstrate a sensitive nanoscale manipulation of magnetic properties, shedding light on magnetic ordering in alloy lattices and broadening the scope for applications.