An understanding of the structural properties that allow for optimal cathode performance, and their origin, is necessary for devising advanced cathode design strategies and accelerating the commercialization of next-generation cathodes. High-voltage, Fe- and Mg-substituted LiNi0.5Mn1.5O4 cathodes offer a low-cost, cobalt-free, yet energy-dense alternative to commercial cathodes. In this work, the effect of substitution on several important structure properties is explored, including Ni/Mn ordering, charge distribution, and extrinsic defects. In the cation-disordered samples studied, a correlation is observed between increased Fe/Mg substitution, Li-site defects, and Li-rich impurity phase formation-the concentrations of which are greater for Mg-substituted samples. This is attributed to the lower formation energy of MgLi defects when compared to FeLi defects. Li-site defect-induced impurity phases consequently alter the charge distribution of the system, resulting in increased [Mn3+] with Fe/Mg substitution. In addition to impurity phases, other charge compensators are also investigated to explain the origin of Mn3+ (extrinsic defects, [Ni3+], oxygen vacancies and intrinsic off-stoichiometry), although their effects are found to be negligible.