Magnetite nanoparticles possess numerous fundamental, biomedical, and industrial applications, many of which depend on tuning the magnetic properties. This is often achieved by the incorporation of trace and minor elements into the magnetite lattice. Such incorporation was shown to depend strongly on the magnetite formation pathway (i.e., abiotic vs biological), but the mechanisms controlling element partitioning between magnetite and its surrounding precipitation solution remain to be elucidated. Here, we used a combination of theoretical modeling (lattice and crystal field theories) and experimental evidence (high-resolution inductively coupled plasma–mass spectrometry and X-ray absorption spectroscopy) to demonstrate that element incorporation into abiotic magnetite nanoparticles is controlled principally by cation size and valence. Elements from the first series of transition metals (Cr to Zn) constituted exceptions to this finding, as their incorporation appeared to be also controlled by the energy levels of their unfilled 3d orbitals, in line with crystal field mechanisms. We finally show that element incorporation into biological magnetite nanoparticles produced by magnetotactic bacteria (MTB) cannot be explained by crystal–chemical parameters alone, which points to the biological control exerted by the bacteria over the element transfer between the MTB growth medium and the intracellular environment. This screening effect generates biological magnetite with a purer chemical composition in comparison to the abiotic materials formed in a solution of similar composition. Our work establishes a theoretical framework for understanding the crystal–chemical and biological controls of trace and minor cation incorporation into magnetite, thereby providing predictive methods to tailor the composition of magnetite nanoparticles for improved control over magnetic properties.