The indirect determination of the most used herbicide worldwide, glyphosate, was achieved by the SERS technique using hemin chloride as the reporter molecule. An incubation process between hemin and glyphosate solutions was required to obtain a reproducible Raman signal on SERS substrates consisting of silicon decorated with Ag nanoparticles (Si-AgNPs). At 780 nm of excitation wavelength, SERS spectra from hemin solutions do not show extra bands in the presence of glyphosate. However, the hemin bands increase in intensity as a function of glyphosate concentration. This allows the quantification of the herbicide using as marker band the signal associated with the ring breathing mode of pyridine at 745 cm−1. The linear range was from 1 × 10−10 to 1 × 10−5 M and the limit of detection (LOD) was 9.59 × 10−12 M. This methodology was successfully applied to the quantification of the herbicide in honey. From Raman experiments with and without silver nanoparticles, it was possible to state that the hemin is the species responsible for the absorption in the absence or the presence of the herbicide via vinyl groups. Likewise, when the glyphosate concentration increases, a subtle increase occurs in the planar orientation of the vinyl group at position 2 in the porphyrin ring of hemin over the silver surface, favoring the reduction of the molecule. The total Raman signal of the hemin-glyphosate incubated solutions includes a maximized electromagnetic contribution by the use of the appropriate laser excitation, and chemical contributions related to charge transfer between silver and hemin, and from resonance properties of Raman scattering of hemin. Incubation of the reporter molecule with the analyte before the conjugation with the SERS substrate has not been explored before and could be extrapolated to other reporter-analyte systems that depend on a binding equilibrium process.