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A side-by-side comparison of softwood (pine) vs hardwood (eucalyptus) pretreatment using 3 protic, 3 aprotic, and 3 choline-derived ionic liquids (ILs) is proposed. While the protic ionic liquid 2-hydroxyethylammonium formate leads to alkali lignin dissolution at 30 °C after 1 h, the lack of interactions with the whole-cell wall limits the biomass disruption. On the contrary, the protic ionic liquid 1-methylimidazolium chloride produces a catalytic effect that extracts almost all of the hemicelluloses, and partially the lignin. Remarkable digestibilities are obtained with choline acetate ([Ch][OAc]) in eucalyptus (69%), while in pine, protic, and choline-derived ILs tested do not appear to be real "greener" alternatives to conventional ILs such as 1-ethyl-3methylimidazolium acetate (the highest digestibility, 84%). Solid morphology revealed a smoother surface in pine pretreated with [Mim][Cl], and confocal fluorescence microscopy was used to distinguish surface holocellulose and lignin, highlighting differences in the accessibility of hardwood vs softwood due to the presence of surface lignin. Two-dimensional nuclear magnetic resonance spectroscopy of saccharified samples pretreated with [Ch][OAc] showed the presence of groups derived from acetate. Finally, thermogravimetric analysis and spectroscopy techniques reveal the difficulties in recovering the ionic liquid and conclude a work that describes the strengths and weaknesses of the ILs and biomasses studied.