This paper presents the influence of Mn2+ substitution by Ni2+ on the structural, morphological and magnetic properties of Mn1−xNixFe2O4@SiO2 (x = 0, 0.25, 0.50, 0.75, 1.00) nanocomposites (NCs) obtained by a modified sol-gel method. The Fourier transform infrared spectra confirm the formation of a SiO2 matrix and ferrite, while the X-ray diffraction patterns show the presence of poorly crystalline ferrite at low annealing temperatures and highly crystalline mixed cubic spinel ferrite accompanied by secondary phases at high annealing temperatures. The lattice parameters gradually decrease, while the crystallite size, volume, and X-ray density of Mn1−xNixFe2O4@SiO2 NCs increase with increasing Ni content and follow Vegard’s law. The saturation magnetization, remanent magnetization, squareness, magnetic moment per formula unit, and anisotropy constant increase, while the coercivity decreases with increasing Ni content. These parameters are larger for the samples with the same chemical formula, annealed at higher temperatures. The NCs with high Ni content show superparamagnetic-like behavior, while the NCs with high Mn content display paramagnetic behavior.