The aim of this study was to investigate the diffusion dynamics of 25% hydrogen peroxide (H2O2) through enamel-dentin layers and to correlate it with dentin’s structural alterations. Micro-Raman Spectroscopy (MRS) and Fourier Transform Infrared Photoacoustic Spectroscopy (FTIR-PAS) were used to measure the spectra of specimens before and during the bleaching procedure. H2O2 was applied to the outer surface of human enamel specimens for 60 minutes. MRS measurements were performed on the inner surface of enamel or on the subsurface dentin. In addition, H2O2 diffusion dynamics from outer enamel to dentin, passing through the dentin-enamel junction (DEJ) was obtained with Raman transverse scans. FTIR-PAS spectra were collected on the outer dentin. MRS findings revealed that H2O2 (O-O stretching µ-Raman band) crossed enamel, had a more marked concentration at DEJ, and accumulated in dentin. FTIR-PAS analysis showed that H2O2 modified dentin’s organic compounds, observed by the decrease in amides I, II, and III absorption band intensities. In conclusion, H2O2 penetration was demonstrated to be not merely a physical passage through enamel interprismatic spaces into the dentinal tubules. H2O2 diffusion dynamics presented a concentration gradient determined by the chemical affinity of the H2O2 with each specific dental tissue.