Mass Spectrometry (MS) is one of the fastest-developing methods in analytical instrumentation. As a highly sensitive, universal detector, it can identify known and unknown compounds, which can indeed be found in a minimal concentration. This review aims to highlight the significant milestones in MS applications in dentistry during recent decades. MS can be applied in three different fields of dentistry: (1) in research of dental materials and chemical agents, (2) in laboratory analysis of biospecimens, and (3) as a real-time diagnostic tool in service of oral surgery and pathology. MS applications on materials and agents may focus on numerous aspects, such as their clinical behavior, possible toxicity, or antimicrobial properties. MS is also a valuable, non-invasive tool for biomarkers’ detection in saliva and has found great application in -omics technologies as it achieves efficient structure-finding in metabolites. As metabolites are located beyond the central dogma, this technique can provide a complete understanding of cellular functions. Thus, it is possible to determine the biological profile in normal and pathological conditions, detect various oral or systematic diseases and conditions, and predict their course. Lastly, some promising advances concerning the surgical approach to potentially oral malignant or malignant disorders exist. This breakthrough method provides a comprehensive approach to dental materials research and biomarker discovery in dental and craniofacial tissues. The current availability of various ‘OMIC’ approaches paves the way for individualized dentistry and provides suggestions for clinical applications in the point-of-care hubs.