Cellulose nanofibrils (CNFs) were obtained by applying a chemical pretreatment consisting of autoclaving the pulp fibers in sodium hydroxide, combined with 2,2,6,6-tetramethylpiperidinyl-1-oxyl-mediated oxidation. Three levels of sodium hypochlorite were applied (2.5, 3.8, and 6.0 mmol/g) to obtain CNF qualities (CNF_2.5, CNF_3.8, and CNF_6.0) with varying content of carboxyl groups, that is, 1036, 1285, and 1593 μmol/g cellulose. The cytotoxicity and skin irritation potential (indirect tests) of the CNFs were determined according to standardized in vitro testing for medical devices. We here demonstrate that autoclaving (121 °C, 20 min), which was used to sterilize the gels, caused a modification of the CNF characteristics. This was confirmed by a reduction in the viscosity of the gels, a morphological change of the nanofibrils, by an increase of the ultraviolet-visible absorbance maxima at 250 nm, reduction of the absolute zeta potential, and by an increase in aldehyde content and reducing sugars after autoclaving. Fourier-transform infrared spectroscopy and wide-angle X-ray scattering complemented an extensive characterization of the CNF gels, before and after autoclaving. The antibacterial properties of autoclaved carboxylated CNFs were demonstrated in vitro (bacterial survival and swimming assays) on Pseudomonas aeruginosa and Staphylococcus aureus. Importantly, a mouse in vivo surgical-site infection model on S. aureus revealed that CNF_3.8 showed pronounced antibacterial effect and performed as good as the antiseptic Prontosan wound gel.