The crystalline sponge method (CSM) is primarily used for structural determination by single‐crystal X‐ray diffraction of a single analyte encapsulated inside a porous MOF. As the host–guest systems often show severe disorder, reliable crystallographic determination is demanding; thus the dynamics of the guest entering and the formation of nanoconfined molecular aggregates has not been in the spotlight. Now, the concept is investigated of the CSM for monitoring the structural evolution of nanoconfined supramolecular aggregates of eugenol guests with displacement of DMF inside the cavities of the flexible MOF, PUM168. The interpretation of the electron density provides a series of unique detailed snapshots depicting the supramolecular guest aggregation, thus showing the tight interplay between the host flexible skeleton and the molecular guests through the DMF‐to‐eugenol exchange process. Solvent‐to‐guest exchange and sliding nets trigger eugenol nanoaggregate formation inside the pores of a flexible pillared metal–organic framework. A detailed description of the different steps of guest aggregation in the nanoconfined environment is furnished by a series of unique crystallographic snapshots.