In recent years, research in the field of protein-based fibrils gained a great attention due to use of these materials as building blocks for construction of functional synthetic biofilms. Yet, efficient and general methodology for preparation of orderly-doped fibrils with desired properties, made of protein-dopant/ligand complexes, still remains a significant challenge. In this manuscript, it is demonstrated that the β-lactoglobulin (β-Lg) protein can form stable and well-defined complexes with linear retinoic acid, discotic protoporphyrine IX and spherical carboxyfullerene ligands (dopants). Upon heating these β-Lg complexes under acidic conditions, formation of orderly-doped fibrils, which partially preserved ligand-specific stoichiometries and modes of binding (of the parent protein-dopant complexes), is observed. These results present a new synthetic methodology, which complements other reported approaches for preparation of the protein-based doped fibrils, by surface functionalization and by post-assembly modulation techniques. A combination of ordered self-assembly nano-structures, with chemical versatility of the orderly-doped protein-based fibrils, represents a new method for construction of novel multifunctional materials in a bottom-up fashion. Preparation of composite β-Lg-complex fibrils by the co-assembly process, using β-Lg building blocks that already incorporate various organic ligands inside, is unprecedented.