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Abstract Two-dimensional van der Waals materials such as graphene present an opportunity for band structure engineering using custom superlattice potentials. In this study, we demonstrate how self-assemblies of magnetic iron-oxide (Fe₃O₄) nanospheres stacked on monolayer graphene generate a proximity-induced magnetic superlattice in graphene and modify its band structure. Interactions between the nanospheres and the graphene layer generate superlattice Dirac points in addition to a gapped energy spectrum near the K and K′ valleys, resulting in magnetic confinement of quasiparticles around the nanospheres. This is evidenced by gate-dependent resistance oscillations, observed in our low temperature transport measurements, and confirmed by self-consistent tight binding calculations. Furthermore, we show that an external magnetic field can tune the magnetic superlattice potential created by the nanospheres, and thus the transport characteristics of the system. This technique for magnetic-field-tuned band structure engineering using magnetic nanostructures can be extended to a broader class of 2D van der Waals and topological materials.