SUMMARY The cleft is an integral part of synapses, yet its macromolecular organization remains unclear. We here show that the cleft of excitatory synapses exhibits a distinct density profile as measured by cryo-electron tomography (cryo-ET). Aiming for molecular insights, we analyzed the synapse-organizing proteins SynCAM 1 and EphB2. Cryo-ET of SynCAM 1 knock-out and overexpressor synapses showed that this immunoglobulin protein shapes the cleft’s edge. In agreement, SynCAM 1 delineates the postsynaptic perimeter as determined by immuno-electron microscopy (EM) and superresolution imaging. In contrast, the EphB2 receptor tyrosine kinase is enriched deeper within the postsynaptic area. Unexpectedly, SynCAM 1 can form ensembles proximal to postsynaptic densities, and synapses containing these ensembles were larger. Postsynaptic SynCAM 1 surface puncta were not static but became enlarged after a long-term depression paradigm. These results support that the synaptic cleft is organized on a nanoscale into sub-compartments marked by distinct trans-synaptic complexes.