Evolution of the local environment of Fe3+ ions in deposited Fe2O3/SiO2 nanoparticles formed in samples with different iron contents was investigated in order to establish the conditions for obtaining the stable ε-Fe2O3/SiO2 samples without impurities of other iron oxide polymorphs. Microstructure of the samples with an iron content of up to 16% is studied by high-resolution transmission electron microscopy, X-ray diffraction analysis, and Mössbauer spectroscopy, and their magnetic properties are examined. At iron concentrations below 6%, calcinations of iron-containing precursor nanoparticles in a silica gel matrix lead to the formation of the ε-Fe2O3 iron oxide polymorphic modification without foreign phase impurities, while at the iron concentration in the range of 6–12%, the hematite phase forms in the sample in the fraction of no more than 5%. It is concluded on the basis of the data obtained that the spatial stabilization of iron-containing particles is one of the main factors facilitating the formation of the ε-Fe2O3 phase in a silica gel matrix without other iron oxide polymorphs. It is demonstrated that the increase in the iron content leads to the formation of larger particles in the sample and gradual changes of the Fe3+ ion local environment during the phase transition ε-Fe2O3 → α-Fe2O3.