In this study, bioactive composite systems based on natural polymers (chitosan and lignin) were prepared in this study. The structural, mechanical, and morphological properties of chitosan-based materials containing various amounts of lignin filler were investigated. The infra-red IR spectroscopy data confirmed the formation of chemical bonds between the components of the obtained composites. The mechanical properties of film samples were studied in air and in physiological solution. It was demonstrated that the breaking elongation values of the obtained film samples in the wet state were higher (150–160%) than the corresponding (average) value of a pure chitosan film (100%). The scanning electron microscopy and atomic force microscopy data demonstrated that the introduction of lignin had caused significant changes in the surface morphology of films. The appearance of a strongly pronounced texture and porosity facilitated cell proliferation on the surface of composites, i.e., the bioactivity of film samples was enhanced with an increasing lignin content in the chitosan matrix.