Three kinds of magnesium-based spinel nanoferrites with the chemical formulas of MgFe2O4 (Mg ferrite), Mg0.9Mn0.1Fe2O4 (Mg-Mn ferrite), and Mg0.9Mn0.1In0.1Fe1.9O4 (Mg-Mn-In ferrite) were synthesized by hydrothermal route. We report the composition-dependent magnetic parameters and microwave properties of Mg-based ferrite nanoparticles. XRD results revealed that the Mg-based ferrite nanoparticles exhibited a cubic spinel structure and had an average nanocrystallite size in the range of 5.8–2.6 nm. Raman spectroscopy analysis confirmed the formation of cubic-spinel phase Mg-based nanoferrites. The room-temperature magnetization measurements indicated that the Mg ferrite nanoparticles had superparamagnetic behavior; whereas the Mg-Mn and Mg-Mn-In ferrite nanoparticles exhibited a paramagnetic nature. The microwave properties of obtained ferrite nanoparticles were studied by alternating current (AC) magnetic susceptibility measurement and electron paramagnetic resonance (EPR) spectroscopy. It was found that the un-substituted Mg ferrite sample exhibited microwave characteristics better than those of the Mn substituted and Mn-In co-substituted Mg ferrite samples.