Recently, filter paper (FP)-based surface-enhanced Raman scattering (SERS) substrates have stimulated significant attention owing to their promising advantages such as being low-cost, easy to handle, and practically suitable for real-field applications in comparison to the solid-based substrates. Herein, a simple and versatile approach of laser-ablation in liquid for the fabrication of silver (Ag)-gold (Au) alloy nanoparticles (NPs). Next, the optimization flexible base substrate (sandpaper, printing paper, and FP) and the FP the soaking time (5–60 min) was studied. Further, the optimized FP with 30 min-soaked SERS sensors were exploited to detect minuscule concentrations of pesticide (thiram-50 nM), dye (Nile blue-5 nM), and an explosive (RDX-1,3,5-Trinitroperhydro-1,3,5-triazine-100 nM) molecule. Interestingly, a prominent SERS effect was observed from the Au NPs exhibiting satisfactory reproducibility in the SERS signals over ~1 cm2 area for all of the molecules inspected with enhancement factors of ~105 and relative standard deviation values of <15%. Furthermore, traces of pesticide residues on the surface of a banana and RDX on the glass slide were swabbed with the optimized FP substrate and successfully recorded the SERS spectra using a portable Raman spectrometer. This signifies the great potential application of such low-cost, flexible substrates in the future real-life fields.