Shank3 is a synaptic scaffolding protein that assists in tethering and organizing structural proteins and glutamatergic receptors in the postsynaptic density of excitatory synapses. The localization of Shank3 at excitatory synapses and the formation of stable Shank3 complexes is regulated by the binding of zinc to the C-terminal sterile-alpha-motif (SAM) domain of Shank3. Mutations in the SAM domain of Shank3 result in altered synaptic function and morphology, and disruption of zinc in synapses that express Shank3 leads to a reduction of postsynaptic proteins important for synaptic structure and function. This suggests that zinc supports the localization of postsynaptic proteins via Shank3. Many regions of the brain are highly enriched with free zinc inside glutamatergic vesicles at presynaptic terminals. At these synapses, zinc transporter 3 (ZnT3) moves zinc into vesicles where it is co-released with glutamate. Alterations in ZnT3 are implicated in multiple neurodevelopmental disorders, and ZnT3 knock-out (KO) mice - which lack synaptic zinc - show behavioral deficits associated with autism spectrum disorder and schizophrenia. Using male and female mice, we show that ZnT3 KO mice have smaller dendritic spines and miniature excitatory postsynaptic current amplitudes than wildtype (WT) mice in the auditory cortex. Additionally, spine size deficits in ZnT3 KO mice are restricted to synapses that express Shank3. In WT mice, synapses that express both Shank3 and ZnT3 have larger spines compared to synapses that express Shank3 but not ZnT3. Together these findings suggest a mechanism whereby presynaptic ZnT3-dependent zinc supports postsynaptic structure and function via Shank3 in a synapse-specific manner.Significance Statement Shank3 is a scaffolding protein that assists in the organization of glutamatergic receptors in the postsynaptic density of excitatory synapses in the brain. The structure and function of Shank3 is regulated by zinc ions. Specifically, zinc allows Shank3 to form tight sheets that assist in stabilizing the postsynaptic density. Zinc packaged by the zinc transporter ZnT3 which is released from presynaptic terminals may contribute to the function of Shank3. In this study, we find an association between ZnT3, Shank3, synaptic strength, and spine size, suggesting that zinc released from presynaptic terminals supports dendritic spine structure and function via interactions with Shank3.