Septins are conserved filamentous GTP-binding proteins that assemble at membranes and cytoskeletal interfaces, yet how they organize neuronal architecture in vivo remains incompletely understood. In neurons, microtubule organization is central to polarity, transport, and synaptic function, but the contribution of septin complexes to microtubule-dependent synaptic architecture remains unclear. Using the genetically tractable and paralog-restricted septin system of Drosophila melanogaster, we dissect the roles of Sep2 and Sep5 at larval neuromuscular junctions. Through integrated genetic, behavioral, immunostaining, and transcriptomic analyses, we show that septin loss disrupts pre- and postsynaptic organization and vesicle recycling while altering microtubule architecture. Notably, loss of septins shifts microtubules toward an acetylated and stabilized state, accompanied by increased expression of microtubule-associated and stabilization-linked factors, including tau, among the most upregulated genes and ringmaker, consistent with enhanced microtubule stabilization. Together, these findings position septin complexes as structural organizers that buffer microtubule state to preserve synaptic architecture, establishing septin composition as a key determinant of neuronal cytoskeletal organization in vivo.