arXiv2026
Magnetic topological insulators offer a platform to control electronic topology through magnetic order, yet reliable routes to tune their properties remain limited. Here, we show that ion irradiation allows to modify the magnetic and the topological properties of the van der Waals magnetic topological insulator MnBi$_2$Te$_4$. Using inert ion beams, intrinsic defects are introduced via collision cascades without chemical doping. We identify two distinct regimes. At low fluence, cation antisite disorder leads to a near-complete redistribution of Bi over cation sites while preserving long-range crystallographic order, accompanied by a transition from $p$-type to $n$-type transport. At high fluence, cation-anion intermixing drives the formation of a previously unreported layer-disordered phase characterized by a high density of van der Waals-specific planar defects, including swapped bilayers. Despite significant structural disorder, the system retains partial periodic order up to high displacement levels. Magnetometry and X-ray spectroscopy show that the Mn high-spin state and antiferromagnetic interactions persist, while magnetic anisotropy is strongly reduced. At the same time, the anomalous Hall conductivity is suppressed fivefold, far exceeding the change in magnetization, indicating a direct modification of Berry curvature. These results establish ion irradiation as a means to tune topology through defect engineering and reveal a disorder-driven approach to control symmetry and electronic structure in van der Waals magnetic materials.