Biodiesel can be produced from ecological friendly processes using edible or waste vegetable oil. Actual production processes can be improved by using heterogeneous catalysts for transesterification reaction activation at low temperature. Few structured or particulated solids with high catalytic activity for biodiesel production reaction have been studied in bibliography. In this work, a microstructured catalyst based on catalytically active pumice material has been developed. Catalytic particles have been made with the shape of an organic template used as former. A novel methodology was used to control the fabrication of pumice-based heterogeneous catalysts as an effective way to improve their efficiency in the production of biodiesel in a continuous packed-bed industrial reactor. The catalytic packed bed reactor configuration studied shows high yields in biodiesel production, obtaining advantages from the microstructural engineering of the catalytic material.