The application of anaerobic digestion technology is growing worldwide, mainly because of its environmental benefits. Nevertheless, anaerobic degradation is a rather slow and sensitive process. One of the reasons is the recalcitrance nature of certain fractions of the substrate (e.g., lignocelluloses) used for microbial degradation; thus, the hydrolysis becomes the rate-limiting step. The other reason is that the degradation of organic matter is based on a highly dynamic, multi-step process of physicochemical and biochemical reactions. The reactions take place in a sequential and parallel way under symbiotic interrelation of a variety of anaerobic microorganisms, which all together make the process sensitive. The first stage of the decomposition of the organic matter is performed by fast growing (hydrolytic and acid forming) microorganisms, while in the second stage the organic acids produced are metabolized by the slow growing methanogens, which are more sensitive than the acidogens; thus, methanogenesis becomes the rate-limiting step. The first part of this work evaluates the effects of a pretreatment using an organic solvent, N-methylmorpholine-N-oxide (NMMO), on cellulose-based materials in order to overcome the challenge of biomass recalcitrance and to increase the rate of the hydrolysis. NMMO-pretreatment of straw separated from the cattle and horse manure resulted in increased methane yields, by 53% and 51%, respectively, in batch digestion tests. The same kind of pretreatment of the forest residues led to an increase by 141% in the methane production during the following batch digestion assays. The second part of this work evaluates the efficacy of a two-stage process to overcome the second challenge with methanogenesis as the rate-limiting step, by using CSTR (continuous stirred tank reactors) and UASB (up flow anaerobic sludge blanket) on a wide variety of different waste fractions in order to decrease the time needed for the digestion process. In the two-stage semi-continuous process, the NMMO-pretreatment of jeans increased the biogas yield due to a more efficient hydrolysis compared to that of the untreated jeans. The results indicated that a higher organic loading rate (OLR) and a lower retention time could be achieved if the material was easily degradable. Comparing the two-stage and the single-stage process, treating the municipal solid waste (MSW) and waste from several food processing industries (FPW), showed that the OLR could be increased from 2 gVS/l/d to 10 gVS/l /d, and at the same time the HRT could be decreased from 10 to 3 days, which is a significant improvement that could be beneficial from an industrial point of view. The conventional single stage, on the other hand, could only handle an OLR of 3 gVS/l/d and HRT of 7 days.