Background: Currently, the use of medicinal plants has increased.Artemisiaspecies have been used in several applications, including medicinal use and uses in cosmetics, foods and beverages.Artemisia arborescensL. andArtemisia incultaare part of the Mediterranean diet in the form of aqueous infusions. Herein, we aimed to compare the secondary metabolites of the decoctions and two different extracts (methanolic and aqueous-glycerolic) of these two species, as well as their antioxidant capacity and trace metal levels. Methods: Total phenolic, total flavonoid, total terpenes, total hydroxycinnamate, total flavonol, total anthocyanin contents and antioxidant/antiradical activity were determined, and GC/MS analysis was applied to identify and quantify phenolics and terpenoids. Trace metals were quantified with ICP-MS. Results: Aqueous-glycerolic extracts demonstrated higher levels of total secondary metabolites, greater antioxidant potential and higher terpenoid levels than decoctions and methanolic extracts. Subsequently, the aqueous-glycerolic extract of a particularly high phenolic content was further analyzed applying targeted LC-MS/MS as the most appropriate analytic tool for the determination of the phenolic profile. Overall, twenty-two metabolites were identified. The potential contribution of infusions consumption to metal intake was additionally evaluated, and did not exceed the recommended daily intake. Conclusions: Our results support the use of these two species in several food, cosmetic or pharmaceutical applications.