​In applying a multi-scale spectroscopic and computational approach, we demonstrate that the synthesis of stacked zeolite silicalite-1 nanosheets, in the presence of a long-tail diquaternary ammonium salt surfactant, proceeds through a pre-organised phase in the condensed state. In situ small-angle X-ray scattering, coupled to paracrystalline theory, and backed by electron microscopy, shows that this phase establishes its meso-scale order within the first five hours of hydrothermal synthesis. Quasi in situ vibrational and solid-state NMR spectroscopy reveal that this meso-shaped architecture already contains some elementary zeolitic features. The key to this coupled organisation at both micro- and meso-scale, is a structure-directing agent that is ambifunctional in shaping silica at the meso-scale whilst involved in molecular recognition at the micro-scale. The latter feature is particularly important and requires the structure-directing agent to reside within the silica matrix already at early stages of the synthesis. From here, molecular recognition directs stabilization of precursor species and their specific embedding into a lattice, as shown by force-field molecular dynamics calculations. These calculations, in line with experiment, further show how it is possible to subtly tune both the zeolite topology and aspect ratio of the condensating crystals, by modifying the headgroup of the structure-directing agent.