Vacuolar-type adenosine triphosphatase (v-ATPase) is a multimeric complex that drives the transport of hydrogen ions upon ATP hydrolysis. At lysosomal compartments, v-ATPase mediates the luminal acidification necessary for catabolic processes, such as endocytic degradation and autophagy. Autophagy is particularly relevant for neurons, due to their post-mitotic nature, polarized morphology and high protein load sustaining synaptic activity and plasticity. v-ATPase is additionally expressed by synaptic vesicles, where it creates the proton gradient driving neurotransmitter loading. Alterations in genes encoding v-ATPase subunits or their regulators negatively affect brain development and synaptic function in animal models and are involved in human diseases such as encephalopathies, epilepsy, neurodevelopmental, and neurodegenerative disorders. In particular, deficits in ATP6V1A – encoding for the ubiquitously expressed subunit A of the V1 complex – have been associated with both early-onset epileptic encephalopathy and late onset Alzheimer’s disease thus identifying it as a potential therapeutic target. In this study we modeled loss of function of Atp6v1a in primary murine hippocampal neurons in order to study neuronal morphology and function. Atp6v1a depletion affects neurite elongation, stabilization, and function of excitatory synapses and prevents synaptic rearrangement upon induction of plasticity. These phenotypes are due to impaired lysosomal pH and autophagy progression with accumulation of aberrant lysosomes at neuronal soma and of enlarged vacuoles at synaptic boutons. These data suggest a physiological role of ATP6V1A in the surveillance of synaptic integrity and plasticity and further support the pivotal involvement of lysosomal function and autophagy flux in maintaining proper synaptic connectivity and adaptive neuronal properties.