Metal nanoparticles (NPs) were reported as an efficient matrix for detection of small molecules using laser desorption/ionization mass spectrometry. Their pronounced efficiency is mostly in desorption enhancement, while, in some cases, NPs can facilitate charge transfer to a molecule, which has been reported for alkali metals and silver. In this work, we present the study of the influence of Ag NP size on the laser desorption/ionization mass spectra of a model analyte, the molecule of riboflavin. The NPs were produced by magnetron sputtering-based gas aggregation in a vacuum and mass-filtered before the deposition on substrates. It was found that the utilization of smaller Ag NPs (below 15 nm in diameter) considerably enhanced the molecule desorption. In contrast, the laser irradiation of the samples with larger NPs led to the increased ablation of silver, resulting in [analyte + Ag]+ adduct formation.