Natural populations of Ruta graveolens L. and Artemisia abrotanum L. in northern Saudi Arabia may be a rich source of natural polyphenols with potential biological activities. Therefore, tentative high-performance liquid chromatography−diode array detection was used to analyze the polyphenol contents of leaf extracts. R. graveolens mainly contained the phenolic acids chlorogenic acid and p-coumaric acid and the flavonoids rutoside and quercetin, whereas those of A. abrotanum mainly contained the phenolic acids isochlorogenic acid and rosmarinic acid and the flavonoid quercetin. Leaf extracts of both species showed antioxidant activities due to the presence of quercetin, chlorogenic acid, and p-coumaric acid as well as antiproliferative and cytotoxic activities against cancer cells, which may be attributed to necrotic cell accumulation during the early and late apoptotic periods. Both species also exhibited antibacterial activity, although the activity was higher in R. graveolens due to the high contents of quercetin and other polyphenols. Finally, both species exhibited antifungal activities, which were associated with specific polyphenols. This is the first study to confirm the richness of polyphenols and wide spectrum of biological activities in natural populations of R. graveolens and A. abrotanum in northern Saudi Arabia.