Intercalation raises manifold possibilities to manipulate the properties of two-dimensional (2D) materials1, and its impact on local electronic/magnetic properties has drawn much attention with the rise of nano-structured 2D materials2,3. Typically, changing an ionic state in a solid involves a dramatic local change of energy as well as orbital/spin magnetic moment from its ground state. However, the atomic investigation of the charging process of an intercalant ion in 2D material has never been explored while such subject has been studied in artificially deposited atoms on thin insulating 2D layers using scanning probe microscopy4–7. Herein, we demonstrate an atomical manipulation of the charge and spin state of Co ions on a metallic NbS2, obtained by cleaving of Co-intercalated NbS2. Density functional theory investigation of various Co configurations reveals that the charging is possible due to a change in the crystal field at the surface and a significant coupling between NbS2 and intercalants occurs via orbitals of the a1g symmetry. The results can be generalized to numerous other combinations of intercalants and base matrixes, suggesting that intercalated transition metal dichalcogenides can be a new platform to introduce single-atom operation 2D electronics/spintronics.