Nanoscale surface patterning and polymerization of caffeic acid on 4-aminothiophenol-functionalized gold surfaces has been demonstrated with dip pen nanolithography (DPN). The diphenolic moiety of caffeic acid can be polymerized by biocatalysis with laccase or horseradish peroxidase. In the present study, the DPN patterned features were polymerized in situ through the use of the peroxidase. Using samples prepared by DPN, microcontact printing, and adsorption on macroscopic substrates, the products were characterized by electrostatic force microscopy (EFM), MALDI-TOF, X-ray photoelectron spectroscopy (XPS), UV-vis, and FT-IR. The in situ surface polymerization resulted in the formation of a quinone structure, while the phenyl ester formed in bulk polymerization reactions was not detected. A different coupling site was observed when comparing the polymers obtained from solution (bulk) vs the surface DPN reactions. The structural differences were attributed to surface-induced pre-organization and orientation of the monomers prior to the enzymatic polymerization step. The results of this study expand the application of DPN technology to surface modification and surface chemistry reactions wherein stereo-regularity and regioselectivity can be exploited.