The methods for hydrogen yield efficiency improvements, the gaseous stream purification in gaseous biofuels generation, and the biomass pretreatment are considered as the main trends in research devoted to gaseous biofuel production. The environmental aspect related to the liquid stream purification arises. Moreover, the management of post-fermentation broth with the application of various biorefining techniques gains importance. Chemical compounds occurring in the exhausted liquid phase after biomass pretreatment and subsequent dark and photo fermentation processes are considered as value-added by products. The most valuable are furfural (FF), 5-hydroxymethylfurfural (HMF), and levulinic acid (LA). Enriching their solutions can be carried with the application of liquid–liquid extraction with the use of a suitable solvent. In these studies, hydrophobic deep eutectic solvents (DESs) were tested as extractants. The screening of 56 DESs was carried out using the Conductor-like Screening Model for Real Solvents (COSMO-RS). DESs which exposed the highest inhibitory effect on fermentation and negligible water solubility were prepared. The LA, FF, and HMF were analyzed using FT-IR and NMR spectroscopy. In addition, the basic physicochemical properties of DES were carefully studied. In the second part of the paper, deep eutectic solvents were used for the extraction of FF, LA, and HMF from post-fermentation broth (PFB). The main extraction parameters, i.e., temperature, pH, and DES: PFB volume ratio (VDES:VPFB), were optimized by means of a Box–Behnken design model. Two approaches have been proposed for extraction process. In the first approach, DES was used as a solvent. In the second, one of the DES components was added to the sample, and DES was generated in situ. To enhance the post-fermentation broth management, optimization of the parameters promoting HMF, FF, and LA extraction was carried under real conditions. Moreover, the antimicrobial effect of the extraction of FF, HMF, and LA was investigated to define the possibility of simultaneous separation of microbial parts and denatured peptides via precipitation.