Intercalation and deintercalation processes in van der Waals crystals underpin their use in nanoelectronics, energy storage, and catalysis but there remains significant uncertainty regarding these materials’ structural and chemical heterogeneity at the nanoscale. Deintercalation in particular often controls the robustness and cyclability of the involved processes. Here, a detailed analysis of potassium ordering and compositional variations in as‐synthesised K intercalated MoS2 as well an analysis of deintercalation induced changes in the structure and K/Mo elemental composition is presented. By combining 4D scanning transmission electron microscopy (4DSTEM), in situ atomic resolution STEM imaging, selected area electron diffraction (SAED) and energy dispersive X‐ray spectroscopy (EDS) the formation of previously unknown intermediate superstructures during deintercalation is revealed. The results provide evidence supporting a new deintercalation mechanism that favors formation of local regions with thermodynamically stable ordering rather than isotropic release of K. Systematic time‐temperature measurements demonstrate the deintercalation behavior to follow first‐order kinetics, allowing compositional and superstructural changes to be predicted. It is expected that the in situ correlative STEM‐EDS/SAED methodology developed in this work has the potential to determine optimal synthesis, processing and working conditions for a variety of intercalated or pillared materials.