Understanding nucleation phenomena is crucial across all branches of physical and natural sciences. Colloidal nanocrystals are among the most versatile and tunable synthetic nanomaterials. While huge steps have been made in their synthetic development, synthesis by design is still impeded by the lack of knowledge of reaction mechanisms. Here, we report on the investigation of the reaction intermediates in high temperature syntheses of copper nanocrystals by a variety of techniques, including X-ray absorption at a synchrotron source using a customized in situ cell. We reveal unique insights into the chemical nature of the reaction intermediates and into their role in determining the final shape of the metal nanocrystals. Overall, this study highlights the importance of understanding the chemistry behind nucleation as a key parameter to predict synthetic pathways for shape-controlled nanocrystals.