We report on monolayer-to-bilayer transitions in 2D metal–organic networks (MONs) from amphiphiles supported at the water–air interface. Functionalized calix[4]arenes are assembled through the coordination of selected transition metal ions to yield monomolecular 2D crystalline layers. In the presence of Ni(II) ions, interfacial self-assembly and coordination yields stable monolayers. Cu(II) promotes 2D coordination of a monolayer which is then diffusively reorganizing, nucleates, and grows a progressive amount of second layer islands. Atomic force microscopic data of these layers after transfer onto solid substrates reveal crystalline packing geometries with submolecular resolution as they are varying in function of the building blocks and the kinetics of the assembly. We assign this monolayer-to-bilayer transition to a diffusive reorganization of the initial monolayers owing to chemical vacancies of the predominant coordination motif formed by Cu2+ ions. Our results introduce a new dimension into the controlled monolayer-to-multilayer architecturing of 2D metal–organic networks.