Spatially defined assembly of colloidal metallic nanoparticles is necessary for fabrication of plasmonic devices. In this study, we demonstrate high-resolution additive jet printing of end-functional polymers to serve as templates for directed self-assembly of nanoparticles into architectures with substantial plasmonic activity. The intriguing aspect of this work is the ability to form patterns of end-grafted poly(ethylene glycol) through printing on a hydrophobic layer that consists of fluoroalkylsilanes. The simultaneous dewetting of the underlying hydrophobic layer together with grafting of the printed polymer during thermal annealing enables fabrication of spatially defined binding sites for assembly of nanoparticles. The employment of electrohydrodynamic jet printing and aqueous inks together with reduction of the feature size during thermal annealing are critically important in achieving high chemical contrast patterns as small as similar to 250 nm. Gold nanospheres of varying diameters selectively bind and assemble into nanostructures with reduced interparticle distances on the hydrophilic patterns of poly(ethylene glycol) surrounded with a hydrophobic background. The resulting plasmonic arrays exhibit intense and pattern-specific signals in surface-enhanced Raman scattering (SERS) spectroscopy. The localized seed-mediated growth of metallic nanostructures over the patterned gold nanospheres presents further routes for expanding the composition of the plasmonic arrays. A representative application in SERS-based surface encoding is demonstrated through large-area patterning of plasmonic structures and multiplex deposition of taggant molecules, all enabled by printing.