Cellulose nanofibrils (CNFs) have emerged as a potential alternative to synthetic polymers in packaging applications owing to their oxygen and grease barrier performance, as well as their strong mechanical properties. However, the performance of CNF films relies on the inherent characteristics of fibers, which undergo changes during the CNF isolation process. Understanding these variations in characteristics during CNF isolation is crucial for tailoring CNF film properties to achieve optimum performance in packaging applications. In this study, CNFs were isolated by endoglucanase-assisted mechanical ultra-refining. The alterations in the intrinsic characteristics of CNFs and their impact on CNF films were systematically investigated by considering the degree of defibrillation, enzyme loading, and reaction time through a design of experiments. Enzyme loading had a significant influence on the crystallinity index, crystallite size, surface area, and viscosity. Meanwhile, the degree of defibrillation greatly affected the aspect ratio, degree of polymerization, and particle size. CNF films prepared from CNFs isolated under two optimized scenarios (casting and coating applications) exhibited remarkable properties, including high thermal stability (approximately 300 °C), high tensile strength (104 – 113 MPa), excellent oil resistance (kit n°12), and low oxygen transmission rate (1.00 – 3.17 cc·m−2.day−1). Therefore, endoglucanase pretreatment can aid in obtaining CNFs with lower energy consumption, resulting in films that possess higher transmittance, superior barrier performance, and reduced surface wettability compared to control samples without enzymatic pretreatment and other unmodified CNF films reported in the literature, all while maintaining mechanical and thermal performance without significant loss.