Intercalation of atoms, ions and molecules is a powerful tool for altering or tuning the properties — interlayer interactions, in-plane bonding configurations, Fermi-level energies, electronic band structures and spin–orbit coupling — of 2D materials. Intercalation can induce property changes in materials related to photonics, electronics, optoelectronics, thermoelectricity, magnetism, catalysis and energy storage, unlocking or improving the potential of 2D materials in present and future applications. In situ imaging and spectroscopy technologies are used to visualize and trace intercalation processes. These techniques provide the opportunity for deciphering important and often elusive intercalation dynamics, chemomechanics and mechanisms, such as the intercalation pathways, reversibility, uniformity and speed. In this Review, we discuss intercalation in 2D materials, beginning with a brief introduction of the intercalation strategies, then we look into the atomic and intrinsic effects of intercalation, followed by an overview of their in situ studies, and finally provide our outlook.