Pretreatment of lignocellulosic biomass with ionic liquids (ILs) is a promising and challenging process for an alternative method of biomass processing. The present work emphasizes the examination of wheat straw pretreatment using ILs, namely, 1-butyl-3-methylimidazolium hydrogensulfate ([bmim][HSO4]), 1-butyl-3-methylimidazolium thiocyanate ([bmim][SCN]), and 1-butyl-3-methylimidazolium dicyanamide ([bmim][N(CN)2]). Only [bmim][HSO4] was found to achieve a macroscopic complete dissolution of wheat straw during pretreatment. The fractionation process demonstrated to be dependent on the IL used. Using [bmim][SCN], a high-purity lignin-rich material was obtained. In contrast, [bmim][N(CN)2] was a good solvent to produce high-purity carbohydrate-rich fractions. When [bmim][HSO4] was used, a different behavior was observed, exhibiting similarities to an acid hydrolysis pretreatment, and no hemicellulose-rich material was recovered during fractionation. A capillary electrophoresis (CE) technique allowed for a better understanding of this phenomenon. Hydrolysis of carbohydrates was confirmed, although an extended degradation of monosaccharides to furfural and hydroxymethylfurfural (HMF) was observed.