The controlled mass transfer across compartmentalised environments in synthetic nanoreactors is essential for enhancing precise spatiotemporal manipulation of chemical transformations within confined spaces. In this study, we present a strategy that integrates a synthetic anion transporter in liposome-based nanoreactors, allowing for spatiotemporal control over the formation of metal–organic complexes in liposomes. This approach enables us to effectively modulate     the assembly of luminescent lanthanide-benzenedicarboxylate nanostructures. Fluorescence studies demonstrate that the reaction rate can be customised by varying the anion transporter concentration, which dictates the rate of entry of the carboxylate ligand. Changes in the morphology of the liposome nanoreactors due to the assisted transmembrane transport of benzenedicarboxylate were investigated using cryo-TEM and time-resolved SAXS measurements, which revealed a structural transformation of the lipid bilayer during the complex formation. Our findings provide a novel platform for exploring coordination chemistry in nanoscale confinements, opening avenues for the design of biohybrid materials.