This study investigated the potential of a novel biomass-derived cork as a suitable catalyst after its modification with Fe@Fe2O3 for in-situ application in heterogeneous electro-Fenton (HEF) process for benzoquinone (BQ) elimination from water. No attempts on the application of modified granulated cork (GC) as a suspended heterogeneous catalyst in the HEF process for water treatment have been published yet. GC was modified by sonification approach in a FeCl3 + NaBH4 solution to reduce the ferric ions to metallic iron in order to obtain Fe@Fe2O3-modified GC (Fe@Fe2O3/GC). Results clearly demonstrated that this catalyst exhibited excellent electrocatalytic properties, such as a high conductivity as well as relatively high redox current and possessed several active sites for water depollution applications. Using Fe@Fe2O3/GC as catalyst in HEF, 100% of BQ removal was achieved in synthetic solutions by applying 33.3 mA cm−2 after 120 min. Different experimental conditions were tested to determine that best possible conditions can be as follow: 50 mmol L−1 Na2SO4 and 10 mg L−1 of Fe@Fe2O3/GC catalyst using Pt/carbon-PTFE air diffusion cell by applying 33.3 mA cm−2. Nevertheless, when Fe@Fe2O3/GC was used in the HEF approach to depollute real water matrices, no complete BQ concentration was removal achieved after 300 min of treatment, achieving between 80 and 95% of effectiveness. Display omitted •Fe@Fe2O3/GC can electro-Fenton activate H2O2 to .•OH.•Homogeneous and surface Fe3+/Fe2+ couples activate H2O2 to .•OH.•Fe@Fe2O3/GC-electro-Fenton mineralizes BQ solution better than EF and EO.