In the present study, a novel magnetic sulfonated solid acid catalyst was synthesized using cassava peel, a biomass waste, by incorporating Fe3O4 nanoparticles. The cassava peel biochar was prepared by slow pyrolysis which was further sulfonated with concentrated H2SO4. The magnetic Fe3O4 nanoparticles synthesized by co-precipitation method was incorporated in the sulfonated biochar by ultrasonication to obtain a magnetized sulfonated biochar catalyst. Fe3O4 nanoparticles give excellent stability as the acid sites on the shell structure are easily accessible to reactant sites and also aids in the separation of the catalyst after the transesterification process. The characterization results confirmed that magnetized sulfonated biochar catalyst contains three functional acidic sites: weak (-OH) and strong (-COOH and -SO3H) acidic groups. The catalytic activity and reusability of the magnetic biocatalyst were investigated by microwave assisted biodiesel production from Millettia pinnata seed oil. The biodiesel yield of 98.7% was obtained under the optimum parametric conditions. The enhanced stability and activity of the magnetic catalyst are due to the strong ionic interactions between particles, high sulfonic acid group density and higher accessibility of reactants towards acidic sites. The reusability of catalyst was studied by using it for five cycles obtaining a yield of more than 75%. The fuel properties of the synthesized biodiesel were found to meet international biodiesel standards.