Bio-sensing techniques utilizing metallic nanoparticles as a probe have gained more and more attention and play today an important role in the detection of bacteria. To date, although several sensing materials have been tested, there is still a long way to go to achieve a fast, low-cost, ultrasensitive and multifunctional substrate suitable for a universal biosensor for detection of bacterial cells. Here, we report a novel probe design based on anisotropic plasmonic nanoparticles organized to a biocompatible 3D bio-inorganic scaffold, i.e., nanoplate-bacteria-nanorod supercrystals (NBNS) with extremely high surface-enhanced Raman spectroscopic (SERS) activity as a model of synergistic plasmonic enhancement from nanoparticles and assembly. This unique structure of nanoparticles incorporated into supercrystal assembly allows efficient detection, identification and classification of cells and bacteria. In this design, the NBNS ensures that the target cells take advantage of the superior multifold increase in Raman scattering signals (electromagnetic enhancement from both types of nanoparticles), due to the geometry of the 3D scaffold. The excellent reproducibility and stability of NBNS substrates were confirmed by comparing the SERS activities of different substrates and analytes. Principal component analysis (PCA) applied to the SERS spectra clearly discriminated the homogeneous bacterial samples and their mixtures. Successful detection and identification of bacteria in model samples consisting of two representative bacteria blends in Fanta soft-drink were demonstrated via plasmonic bio-inorganic scaffold combined with PCA analysis. We believe that this work will greatly facilitate the development of ultrasensitive SERS probes for highly advanced biosensor, pioneering the use of SERS for controlling food safety.