The increasing demand for methane production cannot be satisfied by the use of anaerobic digestion only from waste/wastewater treatment. Perennial energy crops, such as miscanthus and willow, as well as agricultural residues can be considered as options for increasing the methane production through biomass digestion, due to their high organic content and biomass yield. These materials present a great potential, which is only limited by the rigid lignocellulosic structure. In this case, it is possible to apply a pretreatment step in order to achieve increased biogas production. In the present study, aqueous ammonia soaking (AAS) has been investigated as a method to disrupt the lignocellulosic structure and increase the methane yield of wheat straw, miscanthus and willow. Among the three biomasses tested, wheat straw and miscanthus were the most promising in terms of methane production, yielding around 200 and 230 ml of methane per gram of total solids. In all three cases, AAS resulted to an increase in methane yield of 37-41%, 25-27% and 94-162% for wheat straw, miscanthus and willow, respectively. A comparison of the methane yields after 20 and 50 days of anaerobic digestion revealed that AAS affected positively the methane production rate as well. AAS also resulted to a low solubilization of sugars, with a 15.4% and 8.9% increase in soluble xylose concentration in miscanthus and willow, respectively, and a 5% solubilization of glucose in AAS-pretreated miscanthus. © 2013 Taylor and Francis.