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This study introduces a straightforward approach to construct three-dimensional (3D) surface-enhanced Raman spectroscopy (SERS) substrates using chemically modified silica particles as microcarriers and by attaching metal nanoparticles (NPs) onto their surfaces. Tollens’ reagent and sputtering techniques are utilized to prepare the SERS substrates from mercapto-functionalized silica particles. Treatment with Tollens’ reagent generates a variety of silver NPs, ranging from approximately 10 to 400 nm, while sputtering with gold (Au) yields uniformly distributed NPs with an island-like morphology. Both substrates display wide plasmon resonances in the scattering spectra, making them effective for SERS in the visible spectral range, with enhancement factors (ratio of the analyte’s intensity at the hotspot compared to that on the substrate in the absence of metal nanoparticles) of up to 25. These 3D substrates have a significant advantage over traditional SERS substrates because their active surface area is not limited to a 2D surface but offers a much greater active surface due to the 3D arrangement of the NPs. This feature may enable achieving much higher SERS intensity from within streaming liquids or inside cells/tissues.