It is reported that alkali–fullerene plasmas consisting of positive alkali-metal ions, negative fullerene ions, and residual electrons are effective in encapsulating fullerenes inside single-walled carbon nanotubes (SWNTs). When positive or negative bias-voltages are applied to SWNTs in plasmas, accelerated negative fullerene or positive alkali-metal ions are irradiated to the SWNTs through the plasma sheath, respectively. Field emission gun transmission electron microscopy (FEG-TEM) clearly shows that drastic structural modifications such as severe bending of SWNT bundles, tube dislocation, and tube tip termination take place after the ion irradiation. Energy dispersive X-ray spectrometry (EDS) confirms the existence of the alkali-metal elements in the sample after the alkali-metal irradiation. In addition to this, the SWNTs encapsulating fullerene molecules are directly observed after only 1 h fullerene-ion irradiation. These results suggest that our experimental system could permit us to intercalate not only fullerenes but also other elements inside the SWNTs by the applied-bias control. Raman scattering spectroscopy is also adopted for the purpose of evaluating pure SWNTs and fullerene encapsulated SWNTs.