In light of the importance of nanostructured surfaces for a variety of technological applications, the quest for simple and reliable preparation methods of ordered, nanometer ranged structures is ongoing. Herein, a versatile method to prepare ordered, non-close-packed arrangements of nanoparticles on centimeter sized surfaces by self-assembly is described using monodisperse (118–162 nm Ø), amino-functionalized silica nanoparticles as an exploratory example. It is shown that the arrangement of the particles is governed by the interplay between the electrostatic repulsion between the particles and the interaction between particles and surfaces. The latter is tuned by the properties of the particles such as their surface roughness as well as the chemistry of the linkage. Weak dispersive interactions between amino groups and gold surfaces are compared to a covalent amide linkage of the amino groups with carboxylic acid functionalized self-assembled monolayers. It was shown that the order of the former systems may suffer from capillary forces between particles during the drying process, while the covalently bonded systems do not. In turn, covalently bonded systems can be dried quickly, while the van der Waals bonded systems require a slow drying process to minimize aggregation. These highly ordered structures can be used as templates for the formation of a second, ordered, non-close-packed layer of nanoparticles exemplified for larger polystyrene particles (Ø 368 ± 14 nm), which highlights the prospect of this approach as a simple preparation method for ordered arrays of nanoparticles with tunable properties.