In this study, Surface-enhanced Raman Spectroscopy (SERS) and Fourier Transform Infrared Spectroscopy (FTIR) were employed to investigate the molecular changes in Escherichia coli (E. coli) induced by exposure to ampicillin (AMP), enrofloxacin (ENR), ciprofloxacin (CIP), and norfloxacin (NFX) over time. The optimal concentration of E. coli for SERS analysis was determined to be 50 μL of bacterial suspension, diluted six times to achieve an OD600 ≈ 0.1. The primary changes in the SERS spectra were observed at 1267 cm-1, corresponding to the amide III band in proteins, while the FTIR spectra revealed significant changes in the 1200-900 cm-1 range, associated with carbohydrates, under AMP treatment. ENR, CIP, and NFX, which are quinolone antibiotics, act as inhibitors of DNA synthesis. The main changes in the SERS spectra for antibiotic-resistant E. coli were observed at 760 cm-1 (attributed to cytosine and uracil), 960 cm-1 (CN stretching and CC deformation), and 1140 cm-1 (COC stretching and ring breathing). In the FTIR spectra, significant changes were detected at 1655 cm-1, 1544 cm-1, and 1239 cm-1, corresponding to the amide I, amide II, and amide III bands, respectively. The combination of SERS and FTIR with principal component analysis (PCA) enabled the detection of molecular modifications in antibiotic-resistant E. coli exposed to different classes of antibiotics. These findings enhance our understanding of the mechanisms of action of antibiotics in bacteria.