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The use of plasma processes in nanomaterial synthesis is limited by a lack of understanding of the effects of plasma treatment on the morphology and other properties. Here, we studied the effects of atmospheric plasma treatment on the morphology and optical properties of Ag nanoparticles. The Ag nanoparticles were deposited on substrates by injecting an aerosol into flowing argon gas and then treated with a low-temperature atmospheric plasma jet. After plasma treatment, the mean Ag nanoparticle diameter reduced to an average of 5 nm, which was accompanied by a blue shift of ~70 nm in the peak of the surface plasmon resonance; these results are similar to those obtained by thermal treatment at elevated temperatures. The reduction in nanoparticle size is explained by the redox reaction that occurs on the nanoparticle surface, which is evident from the presence of AgO and Ag2O Raman peaks in the treated sample. The surface charge changed as a result of plasma treatment, as indicated by a large change in the zeta potential from +25.1 ± 4 mV for the untreated sample to −25.9 ± 6 mV after 15 min of plasma treatment. Surface-enhanced Raman spectroscopy of the plasma-treated films was carried out with the fluorescent dye Rhodamine 6 G, which showed a ~120-fold enhancement in the signal intensity relative to the untreated substrates. We, therefore, conclude that cold-plasma treatment modified the surface morphology of the Ag nanoparticles, thereby enhancing their optical properties. This technique could be applied to a wide range of nanoparticle systems used in biosensing applications.