We have investigated the early stages of formation of iron oxide nanoparticles from iron stearate precursors in the presence of sodium stearate in an organic solvent by in situ liquid phase transmission electron microscopy (IL-TEM). Before nucleation, we have evidenced the spontaneous formation of vesicular assemblies made of iron polycation-based precursors sandwiched between stearate layers. Nucleation of iron oxide nanoparticles occurs within the walls of the vesicles, which subsequently collapse upon consumption of the iron precursors and growth of the nanoparticles. We then evidenced that fine control of the electron dose, and therefore of the local concentration of reactive iron species in the vicinity of the nuclei, enables controlling crystal growth and selecting the morphology of the resulting iron oxide nanoparticles. Such direct observation of the nucleation process templated by vesicular assemblies in a hydrophobic organic solvent sheds new light on the formation process of metal oxide nanoparticles and therefore opens ways for the synthesis of inorganic colloidal systems with tunable shape and size.