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At present, the widespread use of iron oxide nanoparticles, including for commercial purposes, requires strict preservation of their phase composition during their application. The choice of nanoparticle modifier and modification conditions is decisive due to their high sensitivity to oxygen in the case of using real conditions (O2, pH change, etc.). In this work, we studied the change in the phase composition of magnetite nanoparticles after modification with 3-aminopropyltriethoxysilane (APTES) and oxidation with nitric acid in order to estimate the protective potential of the silica shell. After modification by APTES and oxidation with nitric acid, the nonstoichiometric nature of the magnetite nanoparticles according to XRD data increased, which indicates an increase in transition forms compared to the initial sample (magnetite content decreased to 27% and 24%, respectively). In contrast, Mössbauer spectroscopy data detected a decrease in the nonstoichiometric index due to APTES modification conditions, but strong oxidation after exposure to nitric acid. It also showed that by analyzing the data of the diffraction analysis and Mössbauer spectroscopy for the same sample, one can obtain information not only about the ionic composition of “magnetite”, but also about the distribution of iron ions of different charges over the crystalline and amorphous parts of the preparation.