We investigated the electrochemical lithium-ion storage properties of 9,10-anthraquinone (AQ) and 9,10-phenanthrenequinone (PhQ) molecules encapsulated in the inner hollow core of single-walled carbon nanotubes (SWCNTs). The structural properties of the obtained encapsulated systems were characterized by electron microscopy, synchrotron powder X-ray diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy. We found that almost all quinone molecules encapsulated in the SWCNTs can store Li-ions reversibly. Interestingly, the undesired capacity fading, which comes from the dissolution of quinone molecules into the electrolyte, was suppressed by the encapsulation. It was also found that the overpotential of AQ was decreased by the encapsulation, probably due to the high-electric conductivity of SWCNTs.