Phytochemicals, obtained from natural sources, have high importance for their practical implications owing to their inherent biological characteristics. Naphthoquinone compounds (alkannin and shikonin) from Alkanna tinctoria are well known for antioxidant and coloring properties. Here, naphthoquinone-rich dyeing solution was obtained by aqueous extraction of alkanet roots and applied on protein-based fabrics, i.e., wool. Bioactive colored fabrics were characterized for UV protection, antioxidant activity, and color characteristics. Ultraviolet (UV) protection ability was measured in terms of UV transmittance and UPF (UV protection factor) values, and antioxidant activity in percentage. Some non-hazardous metal salts in permissible concentrations were used as mordants, and their effects on coloration and bioactivities were studied. These salts significantly improved color characteristics and broadened the shade range, while it had little effect on bioactivities. Control dyeing with alkanet extract showed great potential for UV protection and antioxidant activity owing to the conjugated systems in naphthoquinone compounds. Polar functional groups of naphthoquinones were responsible for adsorption on fabric surfaces via chemical interactions.