Collagen in the body is exposed to a range of influences, including free radicals, which can lead to a significant change in its structure. Modeling such an effect on collagen fibrils will allow one to get a native structure in vitro, which is important for modern tissue engineering. The aim of this work is to study the effect of free radicals on a solution of hydrogen peroxide with a concentration of 0.006–0.15% on the structure of collagen fibrils in vitro, and the response of cells to such treatment. SEM measurements show a decrease in the diameter of the collagen fibrils with an increase in the concentration of hydrogen peroxide. Such treatment also leads to an increase in the wetting angle of the collagen surface. Fourier transform infrared spectroscopy demonstrates a decrease in the signal with wave number 1084 cm−1 due to the detachment of glucose and galactose linked to hydroxylysine, connected to the collagen molecule through the -C-O-C- group. During the first day of cultivating ASCs, MG-63, and A-431 cells, an increase in cell adhesion on collagen fibrils treated with H2O2 (0.015, 0.03%) was observed. Thus the effect of H2O2 on biologically relevant extracellular matrices for the formation of collagen scaffolds was shown.