The Asteraceae family has been of significant concern for ethnobotanical studies, thanks to its health-promoting properties linked to a plethora of bioactive compounds, among which phenolic compounds play a critical role. In this work, a workflow based on computational chemometrics was employed to assess the authenticity and biomarker search of five key Asteraceae species commonly employed in traditional medicine. The UHPLC-DAD-ESI/MS-MS phenolic profile of Asteraceae extracts was combined with the evaluation of several in vitro biological properties. Caffeoylquinic acids (CQAs), chicoric acids, and flavonoid glycosides were reported as authenticity markers of Achillea millefolium, Taraxacum officinale, and Arnica montana, respectively. The integration of phenolic profile and in vitro bioactivities provide insights for the identification of trans 3,5-O-dicaffeoylquinic acid (3,5-O-diCQA) and isorhamnetin glycosides as the major antioxidant agents in Asteraceae extracts, whereas several CQAs and caffeoyl-deoxy-octulopyranosonic acids have been reported as responsible for their cytotoxic and anti-inflammatory activities. These results shed light on the authentication and quality evaluation of Asteraceae extracts, along with the characterization of their functional properties, leading to their application in the design of novel plant-based functional foods.