In the current study, surface-enhanced Raman scattering (SERS) was performed to evaluate the antibacterial activity of lab-synthesized drug (1-isopentyl-3-pentyl-1H-imidazole-3-ium bromide salt) and commercial drug tinidazole againstBacillus subtilis. The changes in SERS spectral features were studied for unexposed bacillus and exposed one with various dosages of drug synthesized in the lab (1-isopentyl-3-pentyl-1H-imidazole-3-ium bromide salt), and SERS bands were assigned associated with the drug-induced biochemical alterations in bacteria. Multivariate data analysis tools including principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) have been utilized to analyze the antibacterial activity of the imidazole derivative (lab drug). PCA was employed in differentiating all the SERS spectral data sets associated with the various doses of the labsynthesized drug. There is clear discrimination among the spectral data sets of a bacterial strain treated with different concentrations of the drug, which are analyzed by PLS-DA with 86% area under the curve in receiver operating curve (ROC), 99% sensitivity, 100% accuracy, and 98% specificity. Various dominant spectral features are observed with a gradual increase in the different concentrations of the applied drug including 715, 850, 1002, 1132, 1237, 1396, 1416, and 1453 cm −1 , which indicate the possible biochemical changes caused in bacteria during the antibacterial activity of the lab-synthesized drug. Overall, the findings show that imidazole and imidazolium compounds generated from tinidazole with various alkyl lengths in the amide substitution can be effective antibacterial agents with low cytotoxicity in humans, and these results indicate the efficiency of SERS in pharmaceuticals and biomedical applications.