The main objective of this work was to optimize the process of fractionation of the bagasse of Agave angustifolia Haw, applying organosolv assisted with microwaves. The DCC was used to evaluate the effect of independent variables such as ethanol concentration (40, 50, and 60%) and reaction time (1, 1.5, and 2 h) on yield, cellulose and lignin percentages. Lignocellulosic fractions (F1 and F2) were obtained by means of organosolv assisted with microwave in an open system (atmospheric pressure) and a closed system (controlled pressure). The lignocellulosic fractions were microstructurally characterized. The highest extraction yields (70.39%) were reached in the open system at 50% ethanol for 1.5 h. The highest percentages of LK (5.05%) were obtained in the closed system at 60% ethanol for 2 h. The SEM photomicrograph showed that the microstructure of F1 was retained even after treatment with 60% ethanol for 2 h, and the exposure of the fibrillar part was observed obtaining the disposition of pectin.