AbstractHerein, we show how the chaotropic effect arising from reduced molybdate ions in acidified aqueous solution is able to amplify drastically weak supramolecular interactions. Time‐resolved Small Angle X‐ray Scattering (SAXS) analysis suggests that molybdenum‐blue oligomeric species form huge aggregates in the presence of γ‐cyclodextrin (γ‐CD) which results in the fast formation of nanoscopic {Mo₁₅₄}‐based host‐guest species, while X‐ray diffraction analysis reveals that the ending‐point of the scenario results in an unprecedented three‐component well‐ordered core–shell‐like motif. A similar arrangement was found by using preformed hexarhenium chalcogenide‐type cluster [Re₆Te₈(CN)₆]⁴⁻ as exogenous guest. This seminal work brings better understanding of the self‐assembly processes in general and gives new opportunities for practical applications in the design of complex multicomponent materials via the simplicity of the non‐covalent chemistry.