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Abstract Skyrmions and antiskyrmions are nanoscale swirling textures of magnetic moments formed by chiral interactions between atomic spins in magnetic noncentrosymmetric materials and multilayer films with broken inversion symmetry. These quasiparticles are of interest for use as information carriers in next-generation, low-energy spintronic applications. To develop skyrmion-based memory and logic, we must understand skyrmion-defect interactions with two main goals—determining how skyrmions navigate intrinsic material defects and determining how to engineer disorder for optimal device operation. Here, we introduce a tunable means of creating a skyrmion-antiskyrmion system by engineering the disorder landscape in FeGe using ion irradiation. Specifically, we irradiate epitaxial B20-phase FeGe films with 2.8 MeV Au⁴⁺ions at varying fluences, inducing amorphous regions within the crystalline matrix. Using low-temperature electrical transport and magnetization measurements, we observe a strong topological Hall effect with a double-peak feature that serves as a signature of skyrmions and antiskyrmions. These results are a step towards the development of information storage devices that use skyrmions and antiskyrmions as storage bits, and our system may serve as a testbed for theoretically predicted phenomena in skyrmion-antiskyrmion crystals.