Reusability and durability of catalysts are main factors in biodiesel production. Fe3O4@SiO2‐APTES‐MoO2L2DHAPh catalyst was prepared in five steps. At first, Fe3O4 was synthesized and coated with silica (Fe3O4@SiO2). After that, the nanoparticles were functionalized by APTES (Fe3O4@SiO2‐APTES). In following, DHAPh ligand was anchored covalently onto the surface of aminated magnetic nanoparticles (Fe3O4@SiO2‐APTES‐LDHAPh), and at the end, DHAPh ligand was metalled by MoO2(acac)2 salt (Fe3O4@SiO2‐APTES‐MoO2L2DHAPh). The catalyst was characterized with analytical techniques such as FT‐IR, SEM, TEM, XRD, XPS, VSM, ICP, EDX, NH3‐TPD, and TGA. This novel catalyst with acidic and basic sites was used in (trans)esterification reaction for biodiesel production of rapeseed and other oils. The biodiesel yield of rapeseed, soybean, sunflower, and used frying oils was attained 97%, 98%, 96%, and 87%, respectively, under optimized reaction conditions, such as 0.1 mol% amount of catalyst, 0.05 mmol KOH as methanol activator, a short reaction time of 2 h, and methanol to oil ratio of 3:1 at room temperature. The conversion of oil to methyl ester biodiesel was confirmed by FT‐IR, 1H NMR, and GC‐MS analysis. The leaching and reusability tests of the prepared catalyst were checked, which displayed the biodiesel production proceeded via a heterogeneous pathway. Also, this catalyst can be reused for 11 cycles without tangible loss in its catalytic activity. The mentioned heterogeneously homogenized nanocatalyst has the main benefits such as easy reusability, high activity, and selectivity with acidic and basic sites that makes it a potential candidate for both esterification and (trans)esterification of low quality feedstock for low cost biodiesel production.