In this study, a novel electrocatalytic conversion system via simultaneous esterification and transesterification, based on a ZnAl–layered double hydroxide (LDH)@SiO2, was investigated for fatty acid methyl ester (FAME) production from waste frying oil (WFO). A mechanism is proposed for the (trans)esterification process to generate CH3O− and OH− on the ZnAl–LDH@SiO2 as the semiconductor heterogeneous catalyst. The inclusion of SiO2 enhanced the catalyst's basicity and caused a better exposure of atoms of oxygen atoms on the catalyst's surface which contributed to the formation of methoxides as a nucleophilic attack on the triglyceride's carbonyl. Also, ZnAl–LDH@SiO2 as an electrocatalyst reduces the beginning potential rate and increases the charge carriers transport. The results showed that 98.4% FAME yield was obtained at higher water content from WFO after 90 min of reaction at 25 °C using 2 wt% of the ZnAl–LDH@SiO2 catalyst, and a methanol to WFO (M:WFO) molar ratio of 6:1. ZnAl–LDH@SiO2 was also effective for WFO containing 3.3 wt% of free fatty acid (FFA), and indicated high stability for WFO (trans)esterification after 5 runs. The electrocatalytic conversion system has the potential to advance a new process development for the conversion of feedstock containing high FFA and water to produce the second generation of biodiesel.