Chitosan-based scaffolds modified by gallic acid, ferulic acid, and tannic acid were fabricated. The aim of the experiment was to compare the compatibility of scaffolds based on chitosan with gallic acid, ferulic acid, or tannic acid using the in vivo method. For this purpose, materials were implanted into rabbits in the middle of the latissimus dorsi muscle length. A scaffold based on unmodified chitosan was implanted by the same method as a control. Moreover, the Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR) spectra and scanning electron microscope (SEM) observations were made to study the interactions between chitosan and phenolic acids. Additionally, antioxidant properties and blood compatibility were investigated. The results showed that all studied materials were safe and non-toxic. However, chitosan scaffolds modified by gallic acid and tannic acid were resorbed faster and, as a result, tissues were organized faster than those modified by ferulic acid or unmodified.