While gold nanoparticles (Au NPs) are widely used as surface-enhanced Raman spectroscopy (SERS) substrates, their agglomeration and dynamic movement under laser irradiation result in the major drawback in SERS applications, viz., the repeatability of SERS signals. We tune the optical and structural properties of sizeand shape-modified Au NPs embedded in a thin silicon nitride (Si 3 N 4 ) matrix by intense electronic excitation with swift heavy ion (SHI) irradiation with the aim of overcoming this classical SERS disadvantage. We demonstrate the shape evolution of a single layer of Au NPs inserted between amorphous Si 3 N 4 thin films under fluences of 120 MeV Au 9+ ions ranging between 1 × 10 11 and 1 × 10 13 ions cm −2 . This shape modification results in the gradual blue shift of the localized surface plasmon resonance (LSPR) dip until 1 × 10 12 ions/ cm 2 and then a sudden diminishment at 1 × 10 13 ions/cm 2 . Finite domain time difference (FDTD) simulations further justify our experimental optical spectra. The dynamical NP aggregation and dissolution, in addition to NP elongation and deformation at different fluences, are noted from 2D grazing incidence small-angle X-ray scattering (GISAXS) profiles, as well as cross-sectional transmission electron microscopy (X-TEM). The systematic shape evolution of metal NPs embedded in the insulating matrix is shown to be due to thermal spike-induced localized melting and a localized pressure hike upon SHI irradiation. Utilizing this specific control over the characteristics of Au NPs, viz., shape, size, interparticle gap, and corresponding optical response via SHI irradiation, we demonstrate their applications as very stable SERS substrates, where the separation between NPs and analyte does not alter under laser illumination. Thus, these irradiated SERS active substrates with controlled NP size and gap provide the optimal conditions for creating localized electromagnetic hotspots that amplify the SERS signals, which do not alter with time or laser exposure. We found that the film irradiated with 1 × 10 11 exhibits the highest SERS intensity due to its optimal NP size distribution and shape. Thus, not only our study provides a SERS substrate for stable and repeatable signals but also the understanding depicted here opens new research avenues in designing SERS substrates, photovoltaics, optoelectronic devices, etc. with ion beam irradiation.