The current work focuses on the pretreatment efficiency of ILs combined with heat for woody biomass consisting of spruce, birch and pine as well as winter wheat straw. The latter was investigated as a comparison and with the aim to enhance its digestibility during enzymatic hydrolysis whereby the influence of IL-treatment to cellulose resistance for hydrolysis was investigated. Considering the wood species, the most common and industrially important wood species in Northern Europe were chosen in the present work and the goal was to obtain fermentable sugars and their degradation product, i.e. 5-hydroxymethylfurfural (5-HMF), which is known valuable platform chemical. Further, the differences in the yields of IL-obtainable carbohydrates between these species were studied. The highest sugar yields were obtained to glucose in the case of spruce and arabinose in the case of pine sapwood, 12.07 and 7.72 mmol/L, respectively. The highest 5-HMF yield was obtained for spruce heartwood (9.18 mmol/L) with longer treatment time, such as 100 h. However, regarding woody biomass, the present work was focused more on the study and analysis of the IL-containing liquid part, wood hydrolysate, after IL-treatment aiming to answer the analysis challenges related to this fraction.