The bottom-up synthesis of ligand-stabilised functional nanoparticles from molecular precursors is widely applied but difficult to study mechanistically. Here, we use 31P NMR spectroscopy to follow the trajectory of phosphinate ligands during the synthesis of a range of new ligated zinc oxo clusters, containing 4, 6 and 11 zinc atoms. Using an organometallic route, the clusters interconvert rapidly, and self-assemble in solution based on thermodynamic equilibria, rather than nucleation kinetics. These clusters are also identified, in situ, during the synthesis of phosphinate-capped zinc oxide nanoparticles. Unexpectedly, the ligand is sequestered to a stable Zn11 cluster during the majority of the synthesis and only becomes coordinated to the nanoparticle surface, in the final step. As well as a versatile and accessible route to new (optionally doped) zinc clusters, the findings provide a new understanding of the role of well-defined molecular precursors during the synthesis of small (2-4 nm) nanoparticles.