This work reports on the structural evolution during room temperature synthesis of hexagonally ordered mesoporous silica nanoparticles with and without embedded iron oxide particles. Oleic acid-capped iron oxide nanoparticles are synthesized and transferred to an aqueous phase using the cationic surfactant, hexadecyltrimethylammonium bromide (CTAB). MCM-41 type silica and composite nanoparticles are fabricated via sol–gel synthesis. Aliquots are taken from the solution during synthesis to capture the particle formation process. Transmission Electron Microscopy (TEM) and Small Angle X-ray Scattering (SAXS) reveal a transition from a disordered to an ordered structure in both synthesis systems. Along with the evolution of structure, iron oxide nanoparticles acting as seeds at the early stages are relocated from the particle centers to the edges. Nitrogen sorption measurements for iron oxide-embedded mesoporous nanoparticles indicate surface areas as high as for the mesoporous silica nanoparticles without iron oxide.