The route for the preparation of cellulose nanofiber dispersions from bacterial cellulose using ethylene glycol- or glycerol-based deep eutectic solvents (DES) is demonstrated. Choline chloride was used as a hydrogen bond acceptor and the effect of the combined influence of DES treatment and ultrasound on the thermal and mechanical properties of bacterial cellulose nanofibers (BC-NFs) is demonstrated. It was found that the maximal Young’s modulus (9.2 GPa) is achieved for samples prepared using a combination of ethylene glycol-based DES and ultrasound treatment. Samples prepared with glycerol-based DES combined with ultrasound exhibit the maximal strength (132 MPa). Results on the mechanical properties are discussed based on the structural investigations that were performed using FTIR, Raman, WAXD, SEM and AFM measurements, as well as the determination of the degree of polymerization and the density of BC-NF packing during drying with the formation of paper. We propose that the disordering of the BC-NF surface structure along with the preservation of high crystallinity bulk are the key factors leading to the improved mechanical and thermal characteristics of prepared BC-NF-based papers.