Nanopatterned surfaces enhance incident electromagnetic radiation and thereby enable the detection and characterization of self-assembled monolayers (SAMs), for instance in surface-enhanced Raman spectroscopy (SERS). Herein, Au nanohole arrays, developed and characterized as SERS substrates, are exemplarily used for monitoring a solid-phase deprotection and a subsequent copper(I)-catalyzed azide–alkyne cycloaddition “click” reaction, performed directly on the corresponding SAMs. The SERS substrate was found to be highly reliable in terms of signal reproducibility and chemical stability. Furthermore, the intermediates and the product of the solid-phase synthesis were identified by SERS. The spectra of the immobilized compounds showed minor differences compared to spectra of the microcrystalline solids. With its uniform SERS signals and the high chemical stability, the platform paves the way for monitoring molecular manipulations in surface functionalization applications.