In the current study, the biodiesel fuel generation from waste cooking oil (WCO) as a low-cost feedstock was performed in a T-shaped microreactor through a transesterification process in the presence of binary metal oxide of silver-titanium oxide nanoparticles doped over magnetic graphene oxide (MGO@TiO2Ag) as a novel catalyst. Scanning electron microscopy (SEM), Transform Infrared Spectroscopy (FTIR), vibrating-sample magnetometer (VSM), Energy-Dispersive X-ray Spectroscopy (EDX), and Powder X-ray diffraction (XRD) were employed to characterize the MGO@TiO2Ag nanocatalyst. The Box-Behnken design (BBD) based on the response surface methodology (RSM) was used to optimize the reaction parameters, including methanol to oil volume ratio (Me/Oil), residence time and catalyst concentration. Following data analysis and optimization of the transesterification reaction, the maximum yield of fatty acid methyl esters (FAMEs) which was equal to 96.54 ± 1.16 %, was achieved at the residence time of 169.15 s, Me/Oil ratio of 2.52, and catalyst concentration of 4.15 wt%. All attributes of the manufactured FAMEs were within the permitted ranges of the ASTM D6751 standard, indicating high quality. The finding of this work demonstrated that employing a microreactor has an influential role in producing FAMEs in the presence of an MGO@TiO2Ag nanocatalyst.