Electrophoretic deposition of colloidal nanoparticles shows great promise for the fabrication of nano-structured surfaces, especially relevant for the surface modification of three dimensional medical implants. Here, the role of small and bulky, chemisorbent and physisorbent ligands on metal (gold, platinum) nanoparticle deposition dynamics are systematically investigated. To be able to compare ligand-coated to ligand-free nanoparticles, pulsed laser ablation in liquid is employed as nanoparticle fabrication method. Nanoparticles' electrophoretic properties are assessed via zeta potential measurements and nanoparticle tracking analysis, while online-UV-vis spectroscopy provides information about the deposition dynamics. Electron micrographs and contact angle measurements are employed to characterize the deposit. We show that ligand-free nanoparticles feature a high electrophoretic mobility and linear deposition kinetics, representing an excellent model material for controlled electrophoretic deposition. In contrast, the electrophoretic mobility of surface-modified nanoparticles is altered due to the surrounding ligand layer, resulting in less efficient deposition. Notably, electrophoretic mobility is not solely governed by the ligand's charge and does not correlate to the zeta potential values directly. Finally, bioactive nanotopographies with tunable wettability were created when depositing nanoparticles functionalized with cell-penetrating peptides. These peptide-nanoparticle bioconjugates have great potential to be used for mediating delivery via an implant surface such as a neural electrode. (C) 2015 Published by Elsevier B.V.