Nucleation plays an important role in crystallization outcomes, but it is still poorly understood because it occurs on short timescales and small size scales. Consequently, nucleation mechanisms are still challenging to comprehend and predict. Gaining a better understanding, and potentially control, over nucleation pathways, can significantly aid toward more consistent and targeted crystallization outcomes. To achieve this, facile methods that allow for an accurate depiction and analysis of nucleus‐sized clusters are needed. Herein, the use of crystalline metal–organic frameworks (MOFs) is reported to entrap clusters of small organic molecules, allowing for an accurate representation of the size and shape of the confined clusters via single‐crystal X‐Ray diffraction analysis. This is realized by synthesizing high‐quality single crystals of lanthanum‐based MOFs, which provides well‐defined pore spaces for the encapsulation of guest molecules. The results show that the size and shape of the guest molecular clusters within MOFs significantly differ from their bulk equivalents, suggesting that this method can also be used toward discovering novel polymorphs. Additionally, the findings indicate that these small molecular clusters form via intermolecular interactions that do not always dominate the bulk packing, shedding new light on the initial molecular aggregation mechanisms of precritical nuclei.