A comparative analysis of the response of agave bagasse (AGB) to pretreatment by ammonia fiber expansion (AFEX), autohydrolysis (AH) and ionic liquid (IL) was performed using 2D nuclear magnetic resonance (NMR) spectroscopy, wet chemistry, enzymatic saccharification and mass balances. It has been found that AFEX pretreatment preserved all carbohydrates in the biomass, whereas AH removed 62.4% of xylan and IL extracted 25% of lignin into wash streams. Syringyl and guaiacyl lignin ratio of untreated AGB was 4.3, whereas for the pretreated biomass the ratios were 5.0, 4.2, and 4.7 for AFEX, AH and IL, respectively. Using NMR spectra, the intensity of β-aryl ether units in aliphatic, anomeric, and aromatic regions decreased in all three pretreated samples when compared to untreated biomass. Yields of glucose plus xylose in the major hydrolysate stream were 42.5, 39.7 and 26.9 kg per 100 kg of untreated AGB for AFEX, IL and AH, respectively.