Current economic analysis shows the importance of pretreatment on the overall lignocellulosic ethanol production cost. Understanding the mechanisms by which pretreatment enhances enzymatic hydrolysis can contribute to improved pretreatment methodologies and further reduce pretreatment severity. In this perspective, it is important to determine and characterize the physico-chemical events that occur during pretreatment as a function of its operational parameters. Ammonia Fiber Expansion (AFEX) is a novel pretreatment technology that uses anhydrous ammonia to disrupt the plant cell wall fibers and improve the accessibility of enzymes to their substrates. Ammonia and hydroxyl ions are known to be effective on disrupting ester bonds, which are widely present in the plant cell wall. Some of these ester bonds compose the lignin-carbohydrate complexes (LCC), which are considered to be important structures to maintain the integrity and stability of the plant cell wall. During AFEX pretreatment of Corn Stover, several degradation products were found to be produced. Among these products, acetamide, coumaroyl amide, feruloyl amide and their respective acid counterparts (acetic acid, coumaric acid and ferulic acid) are present in high concentration. Other compounds, such as diferulates were also found to be highly present in the form of amides and/or acids. In this work, we will report the effect of the pretreatment parameters (Temperature, Ammonia Loading, Moisture Content and Residence Time) on the extent of formation of these degradation products which were quantified by LC-MS and GC-MS. The correlation between the extent of formation of these degradation products and enzymatic digestibility of the pretreated biomass will be reported in detail.