By coating plasmonic nanoparticles (NPs) with thermally responsive liquid crystals (LCs) it is possible to prepare reversibly reconfigurable plasmonic nanomaterials with prospective applications in optoelectronic devices. However, simple and versatile methods to precisely tailor properties of liquid-crystalline nanoparticles (LC NPs) are still required. Here, we report a new method for tuning structural properties of assemblies of nanoparticles grafted with a mixture of promesogenic and alkyl thiols, by varying design of the latter. As a model system, we used Ag and Au nanoparticles that were coated with three-ring promesogenic molecules and dodecanethiol ligand. These LC NPs self-assemble into switchable lamellar (Ag NPs) or tetragonal (Au NPs) aggregates, as determined with small angle X-ray diffraction and transmission electron microscopy. Reconfigurable assemblies of Au NPs with different unit cell symmetry (orthorombic) are formed if hexadecanethiol and 1H,1H,2H,2H-perfluorodecanethiol were used in the place of dodecanethiol; in the case of Ag NPs the use of 11-hydroxyundecanethiol promotes formation of a lamellar structure as in the reference system, although with substantially broader range of thermal stability (140 vs. 90 °C). Our results underline the importance of alkyl ligand functionalities in determining structural properties of liquid-crystalline nanoparticles, and, more generally, broaden the scope of synthetic tools available for tailoring properties of reversibly reconfigurable plasmonic nanomaterials.