A woody dicot (hybrid poplar), an herbaceous dicot (goldenrod), and a graminaceous monocot (corn stover) were subjected to alkaline hydrogen peroxide (AHP) pretreatment and subsequent enzymatic hydrolysis in order to assess how taxonomically and structurally diverse biomass feedstocks respond to a mild alkaline oxidative pretreatment and how differing features of the cell wall matrix contribute to its recalcitrance. Using glycome profiling, we determined changes in the extractability of non-cellulosic glucans following pretreatment by screening extracts of the pretreated walls with a panel of 155 cell wall glycan-directed monoclonal antibodies to determine differences in the abundance and distribution of non-cellulosic glycan epitopes in these extracts and assess pretreatment-induced changes in the structural integrity of the cell wall. Two taxonomically-dependent outcomes of pretreatment were identified that both improved the subsequent enzymatic hydrolysis yields but differed in their impacts on cell wall structural integrity. Specifically, it was revealed that goldenrod walls exhibited decreases in all classes of alkali-extractable glycans indicating their solubilization during pretreatment, which was accompanied by an improvement in the subsequent extractability of the remaining cell wall glycans. The corn stover walls did not show the same decreases in glycan abundance in extracts following pretreatment, but rather mild increases in all classes of cell wall glycans, indicating overall weaker associations between cell wall polymers and improved extractability. The hybrid poplar walls were relatively unaffected by pretreatment in terms of composition, enzymatic hydrolysis, and the extractability of cell wall glycans due presumably to their higher lignin content and denser vascular structure.