Great influences of the lowest unoccupied molecular orbital (LUMO) and highest occupied molecular orbital (HOMO) energy levels of the analyte and their alignments compared to the Fermi level of the substrate on the charge transfer (CT) process, and consequently, on the surface-enhanced Raman scattering (SERS) phenomenon have been described via theoretical calculations. To provide experimental evidence, in this study, two antibiotics, chloramphenicol (CAP) and amoxicillin (AMX), were investigated as analytes in SERS sensors based on electrochemically synthesized colloidal silver nanoparticles (e-AgNPs) as the substrate. Despite the same experimental condition, similarities in analyte structure, and in the ability of absorbing onto e-AgNPs, the detection of the two antibiotics showed obvious distinction. While CAP was able to be detected using e-AgNP-based SERS sensors at concentrations down to 1.2 × 10 −9 M, there were no characteristic peaks observed in the SERS spectra of AMX even at a high concentration of 10 −3 M. The LUMO and HOMO energy levels of the two analytes were measured using electrochemical cyclic voltammetry. The obtained results showed that the LUMO levels of both analytes were higher than the Fermi level of Ag, and the LUMO level of AMX was higher than that of CAP. The larger gap between the LUMO level of AMX and the Fermi level of Ag might have prevented the metal-to-molecule CT process, which is related to the Raman signal enhancement in both chemical and electromagnetic mechanisms. In contrast, the smaller energy gap in the case of CAP might have allowed the transfer of hot electrons from the Fermi level of the e-AgNPs to the LUMO level of the analyte. Therefore, CAP could experience an SERS effect on the e-AgNPs under the excitation of a 785 nm laser source, while AMX could not. The hypothesis was then confirmed using three other organic compounds, including furazolidone, 4-nitrophenol, and tricyclazole. The results revealed a clear correlation between the LUMO level of the analytes and their SERS signals.