An analysis on the sustainability of micro-EDM drilling is presented. A process sustainability index was calculated taking into account energy consumption and tool wear during the drilling process. The machining accuracy was also taken into account to calculate the overall sustainability index. The index was validated considering the drilling of three different workpiece materials (stainless steel, tungsten carbide and aluminium) with two electrode materials (brass and tungsten carbide) and different process parameters. An analysis about the influence of workpiece and electrode materials on the sustainability index was carried out. In general, the tool wear has the highest impact on the process sustainability. Considering only the wear and the energy consumption, brass electrode is much more sustainable than the tungsten carbide one for all the tested conditions. This gap is less remarkable if the respect of dimensional tolerances and the consequent percentage of non-conformity is taken into account. From the point of view of the workpiece material, aluminium minimizes the process environmental impact. Finally, the effects on the index of the process parameters, the thermal and electrical characteristics of the electrode and the workpiece materials were evaluated. These results can be useful for approaching a more environmental-oriented strategy in manufacturing.