Understanding the structure and behavior of intermediates in chemical reactions is the key to developing greater control over the reaction outcome. This principle is particularly important in the synthesis of metal nanocrystals (NCs), where the reduction, nucleation, and growth of the reaction intermediates will determine the final size and shape of the product. The shape of metal NCs plays a major role in determining their catalytic, photochemical, and electronic properties and, thus, the potential applications of the material. In this work, we demonstrate that layered coordination polymers, called lamellae, are reaction intermediates in Cu NC synthesis. Importantly, we discover that the lamella structure can be fine-tuned using organic ligands of different lengths and that these structural changes control the shape of the final NC. Specifically, we show that short-chain phosphonate ligands generate lamellae that are stable enough at the reaction temperature to facilitate the growth of Cu nuclei into anisotropic Cu NCs, being primarily triangular plates. In contrast, lamellae formed from long-chain ligands lose their structure and form spherical Cu NCs. The synthetic approach presented here provides a versatile tool for the future development of metal NCs, including other anisotropic structures.