We investigate the quantum dynamics of a harmonic oscillator (HO) system within the framework of topologically charged modified Eddington-inspired Born–Infeld (EiBI) gravity space–time. Additionally, we incorporate the Wu–Yang magnetic monopole (WYMM) into the quantum system and analyze the influences of modified gravity, the topological charge, and WYMM on this HO quantum mechanical system. Using analytical methods, we derive the energy eigenvalues and the corresponding eigenfunctions of the HO. Moreover, we consider a scenario where the modified EiBI-gravity parameter is absent and introduce an inverse square potential, including the WYMM, into the HO system. Our findings show significant deviations in the behavior of the HO system compared to the traditional quantum mechanical HO model, including alterations in the bound-state spectra and eigenfunctions. These results provide valuable insights into the interplay between quantum mechanical problems and alternative gravitational theories.