The interactions of nanoparticles with biomolecules, surfaces, or other nanostructures are dictated by the nanoparticle's surface chemistry. Thus, far, shortcomings of syntheses of nanoparticles with defined ligand shell architectures have limited our ability to understand how changes in their surface composition influence reactivity and assembly. We report new synthetic approaches to systematically control the number (polyvalency), length, and steric interactions of omega-functionalized (targeting) ligands within an otherwise passivating (diluent) ligand shell. A mesofluidic reactor was used to prepare nanoparticles with the same core diameter for each of the designed ligand architectures. When the targeting ligands are malonamide groups, the nanoparticles assemble via cross-linking in the presence of trivalent lanthanides. We examined the influence of ligand composition on assembly by monitoring the differences in optical properties of the cross-linked and free nanoparticles. Infrared spectroscopy, electron microscopy, and solution small-angle X-ray scattering provided additional insight into the assembly behavior. Lower (less than 33%) malonamide ligand densities (where the binding group extends beyond the periphery of diluent ethylene glycol ligands) produce the strongest optical responses and largest assemblies. Surprisingly, nanoparticles containing a higher surface number of targeting ligand did not produce an optical response or assemble, underscoring the importance of an informed mixed ligand strategy for highest nanoparticle performance.