The development of techniques that could be useful in fields other than biological warfare agents countermeasures such as medical diagnostics, industrial microbiology, and environmental applications have become a very important subject of research. Raman spectroscopy can be used in near field or at long distances from the sample to obtain fingerprinting information of chemical composition of microorganisms. In this research, biochemical components of the cell wall and endospores of Bacillus thuringiensis (Bt) were identified by surface-enhanced Raman scattering (SERS) spectroscopy using silver (Ag) nanoparticles (NPs) reduced by hydroxylamine and borohydride capped with sodium citrate. Activation of “hot spots”, aggregation and surface charge modification of the NPs, was studied and optimized to obtain signal enhancements from Bt by SERS. Slight aggregation of the NPs as well as surface charge modification to a more acidic ambient was induced using small-size borohydride-reduced NPs in the form of metallic suspensions aimed at increasing the Ag NP-Bt interactions. Hydroxylamine-reduced NPs required slight aggregation and no pH modifications in order to obtain high spectral quality results in bringing out SERS signatures of Bt.