Intercalation is the insertion of guest species between the planes of a host van der Waals layered crystal. The process is accompanied by a significant change of the charge carrier density and by the expansion of the interlayer distance, overall leading to a modification of the electronic band structure of the layered material. This perspective focuses on the possibilities offered by the intercalation of organic ions toward finely tuning the physical properties of van der Waals materials, in particular their magnetism and superconductivity. How the intercalation of organic ions offers several advantages over conventional guest species such as alkali metals is highlighted, since a careful choice of the molecular intercalant opens the possibility to tailor the interlayer distance and the charge carrier density. Moreover, specific properties of the molecular guest can be transferred to the host material, as recently demonstrated by the intercalation of thermo‐responsive and chiral molecules. It is anticipated that other functional organic ions can be incorporated in van der Waals materials to provide additional optical and magnetic capabilities, with the potential to enable an optical control of magnetism and superconductivity.