Food authentication and fraud detection are global challenges that impact food safety, consumer confidence, and market integrity. Traditional analytical methods often do not provide the speed and accuracy needed to identify adulterations and ensure traceability of food origin. In this context, mass spectrometry (MS) has emerged as an advanced and indispensable approach for food authentication. This chapter explores advanced MS protocols applied to the identification of chemical profiles and characteristic markers in different food categories. Innovative techniques such as ambient ionization mass spectrometry (AIMS), ion mobility mass spectrometry, and proton transfer reaction mass spectrometry are analyzed due to their ability to perform fast, accurate, and nondestructive analyses. Furthermore, the combination of MS with multivariate statistical methods and chemometrics has shown great potential to improve food authenticity screening and adulteration detection. The miniaturization of MS instruments is emerging as a promising trend, enabling more efficient field analysis and inspections in the supply chain. The implementation of these advanced technologies, combined with rigorous validation of analytical models, is essential to ensure reliable interpretations of spectral data. Thus, this chapter provides a comprehensive overview of the state of the art and challenges in the application of MS for food authentication, contributing to the development of robust and efficient protocols for global food safety.