With the aim of bringing the heterogeneous electro-Fenton (EF) treatment one step closer to a more realistic operation, the scaling-up of that technology was evaluated. Assays were performed firstly at lab scale in a stirred-tank reactor and then at bench scale in a flow setup including a jet aerator and a microfluidic flow-through electrochemical cell. A fluidized-bed reactor was added to the bench-scale installation in order to retain the solid catalyst, iron-containing alginate beads. To the best of the authors' knowledge, there are no precedent studies reporting a heterogeneous EF treatment in a similar bench scale-configuration. Hydrogen peroxide generation and clofibric acid removal were assessed at both scales at current intensities of 0.12 and 0.25 A. Results showed that the scaled-up treatment was more efficient and cost-effective: at bench scale 18 times more volume was treated, the mass production of hydrogen peroxide was 28 higher and the specific cost for the removal of clofibric acid was cut by more than half. The most efficient treatment turned out to be the EF performed at 0.12 A at bench scale. Those results highlighted the importance of the reactor design in the scaling-up process. Additionally, aromatic intermediates were detected by liquid chromatography-mass spectrometry (LC-MS) and a degradation route was suggested. Carboxylic acids were also measured by HPLC confirming that the pollutant is mineralizing.