A simple technique is presented to fabricate stable and reproducible plasmonic substrates using chicken eggshell as bio-templates, an otherwise everyday waste material. The 3-dimensional (3D) submicron features on the outer shell (OS), inner shell (IS), and shell membrane (SM) regions are sputter coated with gold and characterized for surface-enhanced Raman scattering (SERS) performance with respect to coating thickness, enhancement factor (EF), hot-spots distribution, and reproducibility. The OS and IS substrates have similar EF (2.6 × 106 and 1.8 × 106, respectively), while the SM provides smaller EF (1.5 × 105) due to its larger characteristic feature size. The variability from them (calculated as relative standard deviation, %RSD) are less than 7, 15, and 9 for the OS, IS, and SM substrates, respectively. Due to the larger EF and better signal reproducibility, the OS region is used for label-free sensing and identification of Escherichia coli and Bacillus subtilis bacteria as an example of the potential SERS applications. It is demonstrated that the detection limit could reach the level of single bacterial cells. The OS and IS regions are also used as templates to fabricate 3D flexible SERS substrates using polydimethylsiloxane and characterized. The simple, low-cost, and green route of fabricating plasmonic substrates represents an innovative alternative approach without the needs for nanofabrication facilities. Coupled with hyperspectral Raman imaging, high-throughput bio-sensing can be carried out at the single pathogen level.