Alpha-synuclein is known to bind to small unilamellar vesicles (SUVs) via its N-terminus which forms an amphipathic alpha-helix upon membrane interaction. Here we show that calcium binds to the C-terminus of alpha-synuclein, therewith increasing its lipid binding capacity. Using CEST-NMR we reveal that alpha-synuclein interacts with isolated synaptic vesicles with two regions, the N-terminus, already known from studies on SUVs, and additionally via its C-terminus, which is regulated by the binding of calcium. Indeed, dSTORM on synaptosomes shows that calcium mediates the localization of alpha-synuclein at the presynaptic terminal, and an imbalance in calcium or alpha-synuclein can cause synaptic vesicle clustering, as seen ex vivo and in vitro. This study provides a new view on the binding of alpha-synuclein to synaptic vesicles, which might also affect our understanding of synucleinopathies.