The effect of SiO2 embedding on the obtaining of single-phase ferrites, as well as on the structure, morphology and magnetic properties of (Zn0.6Mn0.4Fe2O4)δ(SiO2)100−δ (δ = 0–100%) nanoparticles (NPs) synthesized by sol-gel method was assessed. The phase composition and crystallite size were investigated by X-ray diffraction (XRD), the chemical transformations were monitored by Fourier transform infrared (FT-IR) spectroscopy, while the morphology of the NPs by transmission electron microscopy (TEM). The average crystallite size was 5.3–27.0 nm at 400 °C, 13.7–31.1 nm at 700 °C and 33.4–49.1 nm at 1100 °C. The evolution of the saturation magnetization, coercivity and magnetic anisotropy as a function of the crystallite sizes were studied by vibrating sample magnetometry (VSM) technique. As expected, the SiO2 matrix shows diamagnetic behavior accompanied by the accidentally contribution of a small percent of ferromagnetic impurities. The Zn0.6Mn0.4Fe2O4 embedded in SiO2 exhibits superparamagnetic-like behavior, whereas the unembedded Zn0.6Mn0.4Fe2O4 behaves like a high-quality ferrimagnet. The preparation route has a significant effect on the particle sizes, which strongly influences the magnetic behavior of the NPs.