Metal-organic coordination is an attractive means for constructing supramolecular systems, providing versatility, simple synthesis, and a defined geometry. The convenience of changing 'building blocks' during multilayer assembly is exploited for the fabrication of novel ion-coordinated hybrid multilayers on gold. Two bifunctional linkers are used, a tetrahydroxamate and an organic diphosphonate, while the connection between layers is accomplished through Zr(IV) coordination, to form a well-defined hybrid multilayer. The two ion binders are compatible with respect to multilayer assembly, allowing the change of linkers during construction while maintaining the film structural integrity and organization. The different chemical reactivity of the binders enables rational structural manipulation of the multilayer, by selective dissolution of the acid-sensitive hydroxamate layers while keeping the acid-resistant phosphonates (and underlying hydroxamates) intact. The process demonstrates the multilayer structural quality, where two diphosphonate monolayers are capable of effectively blocking proton penetration to underlying hydroxamate layers. This allows nanometer-scale reshaping of the molecular film according to a scheme introduced during its construction.