Magnetic nanocomposites of FeOx@SiO2 and CoFe2O4@SiO2 were prepared via a wet-impregnation route using mesoporous silica nanoparticles as a support matrix. The small pores in the matrix were exploited as nanocavities for controlled growth of the embedded oxide phase, initially examined by introducing different wt% loadings of FeOx in four different samples and sequentially treating them under oxidising and reducing conditions. Comparative examination of the morphological and structural properties of the FeOx@SiO2 compositions shows that a 17 wt% (nominal) loading of the oxide phase, a mixture of Fe3O4 (magnetite) and γ-Fe2O3 (maghemite), is fully embedded within the pores. The 60–70 nm dimensions of the SiO2 nanoparticles are visible in TEM micrographs which reveal a spheroidal shape. TEM also shows a ca. 3 nm size for the crystalline oxide particles embedded within, which agrees with the pore sizes estimated through porosimetric analysis. The measurements for field-cooled (FC), zero-field-cooled (ZFC) magnetizations, and hysteresis loops in the temperature range of 3 K to 300 K reveal that an enhancement in the density of magnetization is obtained for the 17 wt% FeOx@SiO2 sample following reductive thermal treatment. A CoFe2O4@SiO2 nanocomposite prepared with a nominal 14 wt% oxide shows comparable structure and morphology to the 17 wt% FeOx@SiO2 sample, yet superior magnetic properties. The higher density of magnetization in CoFe2O4@SiO2 is attributed to its 40% content of magnetic material in the crystalline phase, versus 6–8% in FeOx@SiO2. Efficient surface functionalisation with APTES, monitored by DRIFT-IR, implies that the magnetic nanocomposites could be used in bio-labelling applications. Data derived from Raman spectroscopy, N2 adsorption/desorption measurements, and TGA are also used to characterise the nanocomposite materials.