Tuning magnetic and electronic transport properties in spinel oxides requires a faithful description between chemical composition and cation site-occupation. Here this challenge is addressed using Fe$_{3-x}$Cr$_x$O$_4$ thin films grown by oxygen-assisted molecular-beam epitaxy within a wide range of composition (0.0 ≤ x ≤ 1.2). Spectroscopic measurements (e.g., X-ray magnetic circular dichroism), refined by theoretical simulations (e.g., crystal field multiplet), are performed to establish a quantitative link between chromium content, Fe2+/Fe3+ site-occupation and macroscopic physical properties of the layers. It is found that Fe$_{3-x}$Cr$_x$O$_4$ thin films (i) delay the transition from inverse to normal spinel configuration with increasing chromium content and (ii) promote collinear spin structure, at odds with bulk material. As a result, strong antiferromagnetic interactions are preserved between spins in tetrahedral and octahedral spinel sublattices, so that chromium-rich thin films exhibit Curie temperatures above room temperature and higher magnetization. Electron hopping is also favored by this singular cation distribution and electronic band gap is smaller than expected for these thin films. The cation site-occupation is therefore a key feature to consider for applications of Fe$_{3-x}$Cr$_x$O$_4$ thin films in spintronics and photocatalysis, as it enables manipulation of magnetic properties (Curie temperature and magnetization) and band gap engineering.