The current biorefineries are focused on the comprehensive fractionation of biomass components into separate lignin and carbohydrate fractions for the production of materials, platform chemicals and biofuel. However, it has become obvious that the combination of lignin and carbohydrates can have significant technical, environmental, and economic benefits as opposed to their separate use. Herein, we developed a green, simple, and flexible biorefinery concept for the integrated utilization of all major biomass components for high-value applications with the focus on functional lignin–carbohydrate hybrids (LCHs). The established process consisted of a modified hydrothermal treatment (HTT) of birch wood followed by solvent extraction of the resulting solids and is therefore named AquaSolv Omni (AqSO) biorefinery. The AqSO biorefinery produces three major streams: hydrolysate (hemicellulose-derived products), solvent-extracted lignin–carbohydrate complexes (LCCs) and cellulose-rich fibers. Specific process conditions were found to facilitate the production of LCCs of different types in high yields as a new valuable and industrially realistic process stream. The effect of the process severity and liquid to solid (L/S) ratio on the yields and compositions of the produced fractions as well as on the structure and properties of the extracted LCCs was investigated using state of the art NMR spectroscopy and molar mass distribution analysis among other methods. The high flexibility of the process allows for engineering of the resulting products in a wide range of chemical compositions, structures and physicochemical properties and therefore gives a good opportunity to optimize the products for specific high-value applications. The process can be easily combined with other biorefinery operations (e.g., enzymatic hydrolysis, pulping, bleaching) to be incorporated into existing value chains or create new ones and thus is suitable for different biorefinery scenarios. First examples of high-value applications of AqSO biorefinery LCHs are reported. LCC nanoparticles (LCCNPs) were produced for the first time directly from the solvent extract and their properties were investigated. LCCNPs could efficiently stabilize Pickering emulsions of tetrahydrofurfuryl methacrylate and allowed their free radical polymerization. In addition, AqSO LCHs showed promising results as wood adhesives. Overall, our results provide detailed information on the complex lignocellulosic fractions and bridge the gap from process engineering to sustainable product development.