In this work, the characteristic structure of keratin extracted from two different kinds of industrial waste, namely sheep wool and chicken feathers, using the sulfitolysis method to allow film deposition, has been investigated. The structural and microscopic properties have been studied by means of scanning electron microscopy (SEM), Raman spectroscopy, atomic force microscopy (AFM), and infrared (IR) spectroscopy. Following this, small-angle X-ray scattering (SAXS) analysis for intermediate filaments has been performed. The results indicate that the assembly character of the fiber can be obtained by using the most suitable extraction method, to respond to hydration, thermal, and redox agents. The amorphous part of the fiber and medium range structure is variously affected by the competition between polar bonds (reversible hydrogen bonds) and disulfide bonds (DB), the covalent irreversible ones, and has been investigated by using fine structural methods such as Raman and SAXS, which have depicted in detail the intermediate filaments of keratin from the two different animal origins. The preservation of the secondary structure of the protein obtained does offer a potential for further application of the waste-obtained keratin in polymer films and, possibly, biocomposites.