Two-dimensional materials such as molybdenum disulfide (MoS2) can be employed as an electrode material in energy systems due its good electrical conductivity and high reachable capacity/capacitance. We demonstrate the concept of a covalent modification of nanostructured MoS2 with anthraquinone (AQ) molecules through diazonium salt chemistry for electrochemical capacitors and lithium-ion storage. AQ molecules are chemically bonded to MoS2 which was proved experimentally by spectroscopic techniques. Here, AQ is grafted (ca. 20 wt%) to the outer surface of nanostructured MoS2, but also confined within the MoS2 interlayer spacing. Modified AQ-MoS2 exhibited faradaic response which improved the overall charge stored from 191 F g−1 (461 F cm−3) to 263 F g−1 (631 F cm−3) at 0.2 A g−1 in 1 M H2SO4. The process of intercalation of ions within interlayer spacing of AQ-MoS2 was not hindered by the presence of confined AQ molecules. Impedance spectroscopy and voltammetry analysis revealed comparable non-diffusion limited response of MoS2 before and after modification. The MoS2 modification was likely conducted on the defect sites limiting the catalytic activity of MoS2 towards hydrogen evolution improving stability of electrodes. In organic medium, the pseudocapacitive response of MoS2, enhanced by additional redox reactions of grafted AQ was observed during lithium-ion storage.