The purpose of this work is to develop a magnetically recoverable magnesium substituted zinc ferrite nanocatalysts for production of biodiesel from waste cooking oil. Microwave assisted combustion process were employed to synthesis the nanocatalyst. The catalyst were characterized by XRD, FTIR, HR-SEM, EDX, DRS and VSM analysis. The VSM study revealed a relatively high magnetic moment and high saturation magnetization property useful for magnetic separation of the catalyst from the reaction medium. Biodiesel conversion of 99.9% was achieved at the optimized reaction conditions like 3 wt% of Mg2+ doped ZnFe2O4 nanocatalyst (ZnMgF5 sample), reaction temperature about 65ᵒC, methanol-oil molar ratio of 18:1 and reaction time 30 min. Investigation on the transesterification kinetics using ZnMgF5 revealed the rate constants ranging from 0.0375 min−1 to 0.2382 min−1, activation energy Eg = 52 kJ mol−1 and frequency factor A = 2.31 × 107 min−1. The negative values of entropy (ΔS°) indicates, increased randomness of the system. Thermodynamic parameters ΔG° = 87.17 kJ mol−1 at 338 K and ΔH° = 49.31 kJ mol−1 indicate that the transesterification reaction is non-spontaneous and endothermic in nature. The magnetically separated catalyst retained 94% of biodiesel yield even after ten cycles of recovery showing a very good performance.