Redox states of flavin mononucleotide (FMN) play important and regulating roles in living systems. To understand the involvement and contribution of FMN coenzyme in different biological processes, probing and characterizing of the associated FMN redox states using powerful experimental approaches are fundamental and crucial. In this study, we have generated a number of typical FMN redox states in Britton–Robinson buffer at different pH environments by applying electric potentials. The electric potential and pH‐dependent events of protonation, deprotonation, and electron transfer process of FMN are probed and characterized by surface‐enhanced Raman spectroscopy (SERS) or resonance SERS (SERRS) using silica coated silver nanoparticles (AgNP@SiO2) as SERS substrate. In addition to experimental SERS analysis, we, using density functional theory, computationally calculated Raman spectra to identify the spectral signatures of the FMN redox‐state sensitive Raman modes. Here, we have specifically probed, analyzed, and characterized signature Raman modes of different redox states of FMN coenzyme including FMNH2•+ (1508‐1510 cm−1), FMNH2 (1512‐1514 cm−1), FMN2−• (1498 cm−1), and FMN3− (1492 cm−1) and proposed the redox reaction schemes of FMN in different experimental conditions.