The sustainable management of natural resources and energy is one of the most important future challenges. This applies in particular for the areas of environmental protection, waste management, renewable energies and climate protection. International and national regulations define a complex system of future objectives, which forces the development of innovations. Anaerobic digestion is a proven technology with great future perspectives in the mentioned field of applications. Experimental results in the included papers are focused on two research areas: Firstly, the optimisation of process chains for the degradation of organic wastes, in particular protein rich by-products and secondly on the treatment of energy crops. The benefits of co-digestion of various waste fractions are compared with the challenges and chances of the mono-digestion of protein rich animal by-products from slaughterhouses. A new stripping process approach for the removal and recovery of ammonia directly out of the digester is proposed for high protein substrate digestion. The second main focus of the included papers is the utilisation of energy crops to biogas. The main goal must be to gain the highest possible methane yield under real process conditions. This is essentially important for the economic success for this new application. The material and energy flows have been balanced at a full scale biogas plant for 20 months. In this time the plant has been operated based on two substrate mixes and without any addition of liquid manure. The higher fibre content of grass and clover compared to the maize plant led to a higher demand for process liquid to dilute the digester content. This causes reduced methane yield, which has to be optimised in near future developments. The topics of basic microbiological research and the challenges at industrial plants have to focus on future goals in environmental protection, waste management, renewable energies and the reduction of green house gas emissions.