Nanostructured core-shell particles with tailor-made affinity surfaces were used to generate microstructured affinity surfaces by microspotting the particles to form densely packed amorphous nanoparticle layers. These layers provided a large reactive surface for the specific binding of protein ligands from aqueous solution. Biofunctional core-shell particles were synthesized for this purpose that consisted of a silica core with a diameter of 100 nm and an organic shell a few nm thick. The nanoparticle core was prepared by sol-gel chemistry and the shell formed in suspension by organosilane chemistry. The shell provided amino groups or carbonyl groups at its outer surface for subsequent covalent immobilization of streptavidin, rabbit IgG antibodies or goat IgG antibodies. AlexaFluor 647-conjugated and biotinylated cytochrome C and CyDye-labeled anti-rabbit IgG and anti-goat IgG were probed as model analytes. The core-shell nanoparticles were spotted using a pin-ring micro-arrayer onto microscope glass slides that were coated with a polycation monolayer by dip-coating prior to nanoparticle deposition. Amorphous particle layers of well-defined thicknesses in the range of 100 nm to 2 microm were obtained by printing aqueous particle suspensions containing 5-500 mg/mL (0.5-50 wt%) of silica particles. The specific affinity of the plotted nanoparticulate capture surface was demonstrated by binding Cy3-labeled donkey anti-rabbit IgG and Cy5-labeled mouse anti-goat IgG to immobilized rabbit IgG and goat IgG particles. The signal intensity per spot increased for any given analyte concentration when the amount of particles per spot was augmented. This was attributed to the increasing integration of receptor molecules per surface footprint, which shifted the binding equilibrium towards the formation of the receptor-ligand complex. Additionally, the locally-increased supply of receptor molecules at the nanoparticulate microchip surface resulted in a wide dynamic range of 4 fM-20 nM (covering six orders of magnitude).