Currently, superparamagnetic functionalized systems of magnetite (Fe3O4) nanoparticles (NPs) are promising options for applications in hyperthermia therapy, drug delivery and diagnosis. Fe3O4 NPs below 20 nm have stable single domains (SSD), which can be oriented by magnetic field application. Dispersion of Fe3O4 NPs in silicon dioxide (SiO2) matrix allows local SSD response with uniaxial anisotropy and orientation to easy axis, 90° <001> or 180° <111>. A successful, easy methodology to produce Fe3O4 NPs (6-17 nm) has been used with the Stöber modification. NPs were embedded in amorphous and biocompatible SiO2 matrix by mechanical stirring in citrate and tetraethyl orthosilicate (TEOS). Fe3O4 NPs dispersion was sampled in the range of 2-12 h to observe the SiO2 matrix formation as time function. TEM characterization identified optimal conditions at 4 h stirring for separation of SSD Fe3O4 in SiO2 matrix. Low magnetization (Ms) of 0.001 emu and a coercivity (Hc) of 24.75 Oe indicate that the embedded SSD Fe3O4 in amorphous SiO2 reduces the Ms by a diamagnetic barrier. Magnetic force microscopy (MFM) showed SSD Fe3O4 of 1.2 nm on average embedded in SiO2 matrix with uniaxial anisotropy response according to Fe3+ and Fe2+ electron spin coupling and rotation by intrinsic Neél contribution.