Herein, we describe the selective positioning of metal-organic framework (MOF) nanoparticles UiO-66 (Universitet i Oslo; Zr6O4(OH)4(bdc)6; bdc2- = benzene-1,4-dicarboxylate) and MIL-101 (Matérial Institut Lavoisier, Cr3O(OH) (H2O)2(bdc)3) at defined positions on a patterned substrate. For this purpose, patterned alkyne- and carboxylic acid-terminated self-assembled organic monolayer (SAM)-modified silicon surfaces were prepared by liquid immersion and microcontact printing (μCP). Preformed UiO-66 and MIL-101 nanometer-sized MOFs (NMOFs) were synthesized by solvothermal synthesis, and the nanocrystallite particles' exterior surface was functionalized in order to generate reactive sites (such as azides and amines) at the NMOFs. Copper-catalyzed alkyne azide cycloaddition and N-hydroxysuccinimide-mediated amide formation were used to selectively position the NMOFs at the surface of pre-patterned substrates. The resulting surfaces were thoroughly investigated by scanning electron microscopy, infrared spectroscopy, and X-ray photoelectron spectroscopy, confirming the validity of the presented approach. We hope that our research paves the way for microsystem integration of NMOFs, for example, in microfluidic devices/reactors, and further investigation of their enhanced catalytic activity.