Surface-functionalized cellulose materials are developed for various purposes, including food additives and food contact materials. A new biologically relevant testing strategy has been developed based on guidance from the European Food Safety Authority to demonstrate the safety of several next-generation surface-functionalized cellulose materials. This strategy involves a complex three-stage simulated digestion to compare the health effects of thirteen novel different types of cellulose. The physical and chemical properties of surface-functionalized fibrillated celluloses differed depending on the type, amount, and location of functional groups such as sulfonate, TEMPO-oxidized carboxy, and periodate-chlorite oxidized dicarboxylic acid celluloses. Despite exposure to gastrointestinal fluids, the celluloses maintained their physicochemical properties, such as negative surface charges and high length-to-width/thickness aspect ratios. An established intestinal co-culture model was used to measure cytotoxicity, barrier integrity, oxidative stress, and pro-inflammatory response to create a toxicological profile for these unique materials. We conclude that the C6 carboxylated cellulose nanofibrils by TEMPO-oxidation induced the most toxicity in the biological model used in this study and that the observed effects were most prominent at the 4-hour post-exposure time point.