Anaerobic digestion is widely applied for the recovery of energy from waste activated sludge. Pre-treatment methods are of high interest to increase the biodegradability of the sludge and to enhance the digestion efficiency. This paper studies the application of a microwave pre-treatment. An experimental set-up of two pilot scale semi-continuous digesters was used. During a long term experiment, one of the reactors was fed with untreated sludge, while microwave pre-treated sludge (336 kJ/kg sludge) was introduced in the second one. A solid retention time of 20 days was kept during the experiments. (Organic) dry solids, carbohydrates, proteins and volatile fatty acids were monitored during digestion. It was seen that the microwave pre-treatment resulted in an effective solubilization of the organic matter in the sludge. The changes to the sludge composition resulted in an increase in biogas production by 50%, while the methane concentration in both reactors remained stable.