In this work, we report the synthesis of hydrated and non-crystalline WO3 flakes (WO3−x) via an environmentally friendly and facile water-based strategy. This method is described, in the literature, as exfoliation, however, based on the results obtained, we cannot say unequivocally that we have obtained an exfoliated material. Nevertheless, the proposed modification procedure clearly affects the morphology of WO3 and leads to loss of crystallinity of the material. TEM techniques confirmed that the process leads to the formation of WO3 flakes of a few nanometers in thickness. X-ray diffractograms affirmed the poor crystallinity of the flakes, while spectroscopic methods showed that the materials after exfoliation were abundant with the surface groups. The thin film of hydrated and non-crystalline WO3 exhibits a seven times higher specific capacitance (Cs) in an aqueous electrolyte than bulk WO3 and shows an outstanding long-term cycling stability with a capacitance retention of 92% after 1000 chronopotentiometric cycles in the three-electrode system. In the two-electrode system, hydrated WO3−x shows a Cs of 122 F g−1 at a current density of 0.5 A g−1. The developed supercapacitor shows an energy density of 60 Whkg−1 and power density of 803 Wkg−1 with a decrease of 16% in Csp after 10,000 cycles. On the other hand, WO3−x is characterized by inferior properties as an anode material in lithium-ion batteries compared to bulk WO3. Lithium ions intercalate into a WO3 crystal framework and occupy trigonal cavity sites during the electrochemical polarization. If there is no regular layer structure, as in the case of the hydrated and non-crystalline WO3, the insertion of lithium ions between WO3 layers is not possible. Thus, in the case of a non-aqueous electrolyte, the specific capacity of the hydrated and non-crystalline WO3 electrode material is much lower in comparison with the specific capacity of the bulk WO3-based anode material.