Biorefineries are plants used for the conversion of renewable biomass into various chemicals, materials, and fuels. The goal of biorefineries is the maximum utilization of all biomass components to produce primary and various secondary products of higher added value. In this research, a new sustainable biorefinery system for the production of biofuels and biochemicals from waste lignocellulosic raw materials was developed. Pre-processing of various lignocellulosic raw materials was performed using physio-chemical and enzymatic methods. In the substrates, obtained after acid hydrolysis of corn cobs in a high-pressure reactor and enzymatic hydrolysis of pre-treated corn cobs, bioprocesses were performed using Mucor indicus DSM 2185 as the working microorganism in three different types of laboratory bioreactors, which resulted in the production of different biochemicals such as bioethanol, xylitol, and glycerol. In addition, by-products of certain processes like the by-products of the enzyme production process or chemical production processes, such as waste media and mold biomass were respectively used, for the production of non-sulfur purple bacteria biomass (pigment isolation) and isopropanol production, and for different biomaterial isolation (chitin, chitosan, and fatty acids) which contributed to the approach of producing a range of different organic products and striving for the principle of so-called zero waste biorefineries. The material balance established that the production of 1 kg of ethanol requires 7,48 kg of corn cobs and 150,35 L of 0.5% sulfuric acid. In addition to ethanol, it is possible to obtain 2.39 kg of isopropanol and 1.27 kg of acetic acid. From the mold and bacterial biomass, it is possible to isolate 0.21 kg of chitin, 0.14 kg of chitosan, 0.18 kg of fatty acids, and 6.73 g of pigments.