In this study we present a new technological approach for the fabrication of ultrapure organically modified gold nanoparticles (AuNPs) for chemical sensing applied to exhaled breath analysis. To achieve a high purity level of the sensing films, we combined Advanced Gas Deposition (AGD) technique to deposit ultrapure monodispersed AuNPs, and dip coating process for functionalization of the AuNPs with thiolated organic ligands. Morphology and surface analysis revealed the deposition of ultrapure isolated AuNPs after the first processing step, and a network of nanoparticle–ligand nanoassemblies after the second processing step. Gas sensing measurements were performed with exhaled breath samples collected from a group of smokers, a group of non-smokers, and ambient air. Sensors responses towards these samples demonstrated characteristic responses for each study group. PCA analysis further revealed samples classification in three distinct characteristic clusters, which indicates the suitability of the molecularly modified AuNPs presented in this communication for breath analysis applications.