Differences in hardwood and softwood, elucidates their behaviour against pretreatments varies. In this work, microwave ionic liquid (IL) and autohydrolysis (AH) pretreatments were applied to Eucalyptus globulus (as a model of hardwood) and Pinus radiata (as a model of softwood). The comparison between hardwood and softwood of microwave ionic liquid (IL) and autohydrolysis (AH) were evaluated in terms of chemical composition of pretreated solids, liquid by streams composition (hemicellulose and lignin extraction) and, substrates enzymatic digestibility. Furthermore, micrographs using scanning electron microscopy (SEM) and confocal fluorescence microscopy supported results obtained. In this study, it has been demonstrated that autohydrolysis pretreatment effectiveness, through maximizing enzymatic digestibility, is opposite in hardwood (73 g glucan/100 g glucan introduced at severe conditions) and softwood (10 g/100 g glucan). IL pretreatment has been especially effective in softwood with higher digestibilities (78 g glucan/100 g glucan introduced) than those obtained in hardwood (68 g glucan/100 g glucan introduced). Confocal fluorescence microscopy images, together with SEM images have resulted to be a clarifying technique to explain enzymatic digestibility results. Final sugars yields after the whole process have shown that low solid yields recoveries obtained in AH treatments have considerably worsened final glucose production, mainly in softwood. IL microwave pretreatment have resulted in higher glucose yields in softwood than in hardwood.