Magnetic nanoparticles as heterogeneous catalysts could open up new possibilities for the development of eco-friendly biodiesel production. In the present study, the Acacia furnesiana (A. furnesiana) fruit component namely pods and seeds are successfully employed as low-cost and environmentally-safe starting materials for the synthesis of NiFe2O4 NPs and also as feedstock for biodiesel synthesis respectively. Interestingly, A. furnesiana seed extract is utilized for the first time as a feed stock for the biodiesel production using NiFe2O4 NPs as catalyst. Using response surface methodology and linear regression, the optimum conditions for the biodiesel production using NiFe2O4 catalyst is obtained. An excellent A. furnesiana oil methyl ester (AFOME)/biodiesel yield of 93.1% is achieved with 4.61 wt% of NiFe2O4 loading, 14:1 M ratio of methanol to oil, 53 min reaction time and at a temperature of 65 °C. The NiFe2O4 catalyst after transesterification reaction is recovered 100% using a permanent magnet and can be reused up to four cycles with > 80% AFOME yield at the end of 4th cycle. The activation energy for AFOME production is found to be ∼ 44.54 kJ/mol from kinetic study and, the thermodynamic investigation revealed that the enthalpy and entropy of the system is ∼ 27.49 kJ/mol and −0.18 kJ mol/k, respectively.