Magnetite (FeO) nanocrystals (MNCs) are among the most-studied magnetic nanomaterials, and many reports of solution-phase synthesis of monodisperse MNCs have been published. However, lack of reproducibility of MNC synthesis is a persistent problem, and the keys to producing monodisperse MNCs remain elusive. Here, we define and explore synthesis parameters in this system thoroughly to reveal their effects on the product MNCs. We demonstrate the essential role of benzaldehyde and benzyl benzoate produced by oxidation of benzyl ether, the solvent typically used for MNC synthesis, in producing monodisperse MNCs. This insight allowed us to develop stable formulas for producing monodisperse MNCs and propose a model to rationalize MNC size and shape evolution. Solvent polarity controls the MNC size, while short ligands shift the morphology from octahedral to cubic. We demonstrate preparation of specific assemblies with these MNCs. This standardized and reproducible synthesis of MNCs of well-controlled size, shape, and magnetic properties demonstrates a rational approach to stabilizing and expanding existing protocols for nanocrystal syntheses and may drive practical advances including enhanced MRI contrast, higher catalytic selectivity, and more accurate magnetic targeting.