Raw materials, such as collagen and chitosan, obtained from by-products from the food industry (beef hides and crustacean exoskeletons), can be used to obtain collagen–chitosan composite biomaterials, with potential applications in regenerative medicine. Functionalization of these composite biomaterials is a possibility, thus, resulting in a molecule with potential applications in regenerative medicine, namely clotrimazole (a molecule with antibacterial, antifungal, and antitumor activity), at a mass ratio (collagen–chitosan–clotrimazole) of 1:1:0.1. This functionalized composite biomaterial has great potential for application in regenerative medicine, due to the following properties: (1) it is porous, and the pores formed are interconnected, due to the use of a mass ratio between collagen and chitosan of 1:1; (2) the size of the formed pores is between 500–50 μm; (3) between collagen and chitosan, hydrogen bonds are formed, which ensure the unity of composite biomaterial; (4) the functionalized bio-composite exhibits in vitro antimicrobial activity for Candida albicans, Staphylococcus aureus, and Staphylococcus aureus MRSA; for the latter microorganism, the antimicrobial activity is equivalent to that of the antibiotic Minocycline; (5) the proliferation tests performed on a standardized line of normal human cells with simple or composite materials obtained by lyophilization do not show cytotoxicity in the concentration range studied (10–500) μg/mL.