Silver nanoparticles (Ag NPs) were fabricated on modified glass substrates to enhance surface-enhanced fluorescence (SEF) using a combination of ion exchange and magnetron sputtering. The ion exchange process, performed prior to sputtering, significantly altered the surface morphology of the Ag NPs, as confirmed by field-emission scanning electron microscopy (FE-SEM). The optical properties of the nanostructures, characterized by UV–Vis spectroscopy, showed an increase in intensity and blue shifts in the localized surface plasmon resonance (LSPR) bands after combining ion exchange and magnetron sputtering. To evaluate SEF performance, fluorescent dyes—Rose Bengal (RB), Eosin Y, and Uranine—were applied to ion-exchanged and bare glass substrates, as well as to 5 nm and 25 nm Ag NPs deposited on both substrate types. Fluorescence emission spectra revealed that the combined use of ion exchange and magnetron sputtering substantially enhanced fluorescence intensity compared to bare glass and to each method applied independently. Enhancement factors reached approximately 2.89-fold for RB, 3.16-fold for Eosin Y, and 9.16-fold for Uranine. These results indicate that the proposed fabrication method is highly effective for SEF applications and holds significant promise for plasmonic-based sensing, particularly in biomedical and biotechnological fields.