White teeth can give confidence and tend to be associated with a healthier lifestyle in modern society. Therefore, modern tooth bleaching strategies have been developed, including the use of hydrogen peroxide and peroxymonosulfate. Although both molecules are oxidizing agents, their effects on the molecular composition of the stained teeth are yet to be determined. In this study, the molecular profiles of teeth bleached with these two different bleaching procedures were compared using liquid chromatography followed by tandem mass spectrometry (LC-MS/MS). GNPS spectral libraries and SIRIUS were used to perform metabolite annotation. The analysis revealed amino acids, dipeptides, and derivatives in peroxymonosulfate and H2O2 treated samples were altered compared to non-bleached sample controls. Additionally, the two bleaching methods led to distinct molecular profiles. For example, diterpenoids were more prevalent after peroxymonosulfate treatment, while treatment with H2O2 resulted in a greater abundance of alkaloids. This work elucidates the biochemical changes resulting from different tooth-whitening strategies.