Detecting fraudulent adulteration of coffee is essential for both the industry and legislative authorities. Both parties are accountable for establishing quality standards through labelling, composition regulations and routine evaluation protocols to circumvent unfair competition among manufacturers as well as to ensure the safety, quality and authenticity of the product for consumers. This chapter addresses current issues in the area of adulteration of coffee as well as describes recent progress on coffee quality evaluation and authentication using the metabolomics approach. The chapter includes a detailed case study on the application of metabolomics to authenticate Asian palm civet coffee and looks ahead to future research trends in this area.