Novel water dispersible large cubic nanocapsules consisting of uniform hydrophobic magnetite core (79 and 126 nm) and amorphous silica shell were prepared. Silica modification of magnetite particles and functionalization of silica surface by introducing methylphosphonate groups were performed at the same time. These nanoparticles were characterized by both transmission and scanning electron microscopy, dynamic light scattering, ζ potential determinations, X-ray techniques, Fourier-transform infrared spectroscopy, and magnetization measurements. The results show that the methodology employed to coat the hydrophobic magnetite with a silica shell provides uniform core–shell magnetite–silica nanoparticles with a good colloidal stability in water and control of the morphology and of the silica thickness. Thus, the high hydrophobicity and strong magnetic dipole interaction of these magnetite nanoparticles are tailored by silica modification, therefore opening a new range of applications in water for these magnetic nanoparticles.