Magnetite is a highly utilized transition metal oxide with many interesting magnetic and transport properties. The presence of anti-phase boundaries (APBs) and charge-orbital ordering (COO) are two of the most exciting properties of epitaxial magnetite thin films. Here, epitaxial stepped Fe₃O₄ films were prepared to investigate the competition between APBs and COO via measurements of in-plane anisotropy. The anisotropy was probed for two orthogonal configurations, with magnetic field applied or electrical-contacts aligned either along or perpendicular to the steps. We reveal that the APBs dominate the magnetic and transport properties of the films above the Verwey transition temperature ([Formula: see text]. However, below [Formula: see text] film thickness becomes a decisive factor in determining the magnetic nature of stepped magnetite films, due to its correlation with domain size. When the film is thinner than a critical thickness, the anisotropy is dominated by the APBs, and a higher anisotropy constant and MR ratio are observed when the magnetic field or contacts are oriented along the steps. Conversely, for sufficiently thick films, below [Formula: see text], the magnetic and electrical transport properties are dominated by COO. Thus a higher anisotropy constant and MR ratio are observed when the magnetic field or contacts are oriented perpendicular to the steps.