The unique optoelectronic properties of semiconductor nanocrystals (quantum dots, QDs), have led to many advances in optoelectronic devices, bioimaging, and biosensing. Recent studies have shown that atomically defined, zero-dimensional magic-size clusters (MSCs) play a crucial role during the nucleation and growth of QDs. A major challenge is the preparation of the MSCs in single-ensemble form without coexistence of other-size QDs. Here we present a heat-up one-pot synthesis approach for the preparation of single-sized ZnSe MSCs. By using the thiol ligand 1-dodecanethiol, we could obtain new insights into the complex interplay of precursors and ligands during MSCs formation.