Anaerobic digestion is an already established process but the increasing need of bio‐waste recovery has determined the emergence of new substrates, revamping the research in this field. Contrary to some other European countries, in Portugal this technology is still scarcely in use. Nonetheless, the current legislation endorses this application as a waste management and as an energy recovery process. The rapid growth of the world population, in the past decades, and the economical development of several countries resulted in the production of large amounts of related to food waste and animal manure. These wastes are good substrates for biogas production. This dissertation reports several studies that were performed in order to evaluate and optimize the methane production of organic wastes anaerobic co‐digestion. Emphasis was placed on the role of fatty wastes in the co‐digestion process. Within this scope, a method is described in order to extract, indentify and quantify Long Chain Fatty Acids (LCFA), in both the solid and liquid phase. Moreover, the feasibility of anaerobic digestion of several bio‐wastes that currently are landfilled is also reported. The substrates used during these research studies were as follows: (1) simulated food waste which was made by blending melted pork lard, white cabbage, chicken breast, and potato flakes to simulate lipids, cellulose, protein, and carbohydrates, respectively; (2) food waste, collected in restaurant of the University of Minho; (3) cow manure; (4) oily waste collected in a canned fish processing industry; (5)five wastes from a coffee substitutes production facility and (6) activated sludge. It was observed that food waste composition altered the single biomethanation potential, which implies that anaerobic digestion facilities with large variations in lipids input can have significant changes in process performance. However, whilst imposing transient fluctuations in the fat content of food waste co‐digestion with cow manure, the results proved that cow manure/food waste co‐digestion presents a sufficient buffer capacity to endorse lipids fluctuations, up to concentrations of 7.7 gCODoil/LReactor (55% OilCOD/TotalCOD), maintaining an efficient overall reactor performance and stability, when the total chemical oxygen demand (COD) fed was constant. Codigestion process of cow manure/food waste was improved by addition of oily wastes pulses. The threshold input of oily waste that enhanced the methane production in this co‐digestion process was 12 gCODoil/Lreactor, considering the mixture of lipids present in the oily waste added. This corresponds to a continuous feeding of 10% (Vfood waste/Vmanure) with intermittent oil pulses of 5% (Voil/Vmanure). A pulse feeding of 18 gCODoil/Lreactor induced a persistent process inhibition, detected by the decrease in pH to a minimum of 6.5 and by an increase in the effluent soluble COD and volatile fatty acids. Negative linear correlations between the achieved biomethanation % and the solid‐associated LCFA or palmitic acid (C16:0), allowed to establish threshold values of 180‐220 gCOD‐LCFA/kg TS and 120‐150 gCOD‐C16:0/kg TS, respectively, that should not be surpassed in order to prevent reactor failure. Four of the five assayed wastes from coffee substitutes, are feasible to be co‐digested with activated sludge, instead of landfilled. The coffee substitute solid waste composed of 100% barley is preferable to be co‐digested with the organic fraction of municipal solid waste. Although an alkaline pre‐treatment before co‐digestion with activated sludge is also beneficial to improve methane production, but the cost of this approach should be evaluated.