Atomically precise nanoclusters can be assembled into ordered superlattices with unique electronic, magnetic, optical and catalytic properties. The co-crystallization of nanoclusters with functional organic molecules provides opportunities to access an even wider range of structures and properties, but can be challenging to control synthetically. Here we introduce a supramolecular approach to direct the assembly of atomically precise silver nanoclusters into a series of nanocluster‒organic ionic co-crystals with tunable structures and properties. By leveraging non-covalent interactions between anionic silver nanoclusters and cationic organic macrocycles of varying sizes, the orientation of nanocluster surface ligands can be manipulated to achieve in situ resolution of enantiopure nanocluster‒organic ionic co-crystals that feature large chiroptical effects. Beyond chirality, this co-crystal assembly approach provides a promising platform for designing functional solid-state nanomaterials through a combination of supramolecular chemistry and atomically precise nanochemistry.