In this study, we report the ultra-trace analyte detection from the complex mixtures of contaminants employing hybrid Sn–Au SERS substrates composed of AuNPs deposited on textured Sn substrates fabricated through a laser-ablation synthesis strategy. The hierarchically arranged sharp micro-pyramids with densely decorated micro/nano-surface features were obtained under the optimized fabrication parameters and depicted the highest SERS performance due to the accumulation of AuNPs within nanoscale inter-particle gaps. The versatility of the synthesized hybrid SERS substrates was explored utilizing a wide category of analytes, including organic dyes (MB and DTTCI), explosives (AN and PA), and biomolecules (adenine and l-tryptophan) exhibiting highly reproducible (relative standard deviation < 10%) SERS signals with the limit-of-detection (LOD) down to 0.32 pM, 3.2 fM, 0.37 μM, 2.93 nM, 0.26 nM, and 0.14 μM concentrations, respectively. Furthermore, the developed SERS sensors were tested for the trace-level identification of specific analytes from the interfering signals of background contaminant species. The two-plex simultaneous detection of AN and adenine molecules exhibit one-order higher LOD 1.25 μM and 1.21 nM, respectively, from the interfering fixed MB concentration. We also demonstrate sensitive identification of thiram and RhB molecules from the complex mixtures of real matrices such as apple juice and chili powder with high detection sensitivity. With Sn-TAu substrates, the well-defined SERS features of thiram and RhB molecules from real matrices exhibit >80% overall intensity compared to pure analytes, along with nano-molar detectability.