The fabrication of substrates for Surface Enhanced Raman Scattering (SERS) applications matching the needs for high sensitive and reproducible sensors remains a major scientific and technological issue. We correlate the morphological parameters of silver (Ag) nanostructured thin films prepared by sputter deposition on flat silicon (Si) substrates with their SERS activity. A maximum enhancement of the SERS signal has been found at the Ag percolation threshold, leading to the detection of thiophenol, a non-resonant Raman probe, at concentrations as low as 10−10M, which corresponds to enhancement factors higher than 7 orders of magnitude. To gain full control over the developed nanostructure, we employed the combination of in-situ time-resolved microfocus Grazing Incidence Small Angle X-ray Scattering with sputter deposition. This enables to achieve a deepened understanding of the different growth regimes of Ag. Thereby an improved tailoring of the thin film nanostructure for SERS applications can be realized.