We present a systematic study on the fabrication, characterization of versatile, and low-cost filter paper-based surface-enhanced Raman spectroscopy (SERS) substrates loaded with salt-induced aggregated Ag/Au nanoparticles (NPs). These were demonstrated as efficient SERS substrates for the detection of multiple explosive molecules such as picric acid (5 μM), 2,4-dinitrotoluene (1 μM), and 3-nitro-1,2,4-triazol-5-one (10 μM) along with a common dye molecule (methylene blue, 5 nM). The concentrations of the dye and explosive molecules in terms of mass represent 31.98 pg, 11.45 ng, 1.82 ng, and 13.06 ng, respectively. Silver (Ag) and gold (Au) colloidal NPs were prepared by femtosecond laser (∼50 fs, 800 nm, 1 kHz) ablation of Ag/Au-target immersed in distilled water. Subsequently, the aggregated nanoparticles were achieved by mixing the pure Ag and Au NPs with different concentrations of NaCl. These aggregated NPs were characterized by UV-visible absorption and high-resolution transmission electron microscopy techniques. The SERS substrates were prepared by soaking the filter paper in aggregated NPs. The morphologies of the paper substrates were investigated using field-emission scanning electron microscopy technique. We have achieved superior enhancements with high reproducibility and sensitivity for filter paper substrates loaded with Ag/Au NPs mixed for an optimum concentration of 50 mM NaCl.