Hops (Humulus lupulus L.) and juniper berries (Juniperus communis L.) are two important medicinal plants widely used in the food, beverage, and pharmaceutical industries due to their strong antioxidant capacity, which is attributed to the presence of polyphenols. The present study is conducted to comprehensively characterize polyphenols from hops and juniper berries using liquid chromatography coupled with electrospray-ionization quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF/MS) to assess their antioxidant capacity. For polyphenol estimation, total phenolic content, flavonoids and tannins were measured, while for antioxidant capacity, three different antioxidant assays including the 2,2-diphenyl-1-picrylhydrazyl (DPPH) antioxidant assay, the 2,2-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid (ABTS) radical cation decolorization assay and the ferric reducing-antioxidant power (FRAP) assay were used. Hops presented the higher phenolic content (23.11 ± 0.03 mg/g dw) which corresponded to its strong antioxidant activity as compared to the juniper berries. Using LC-ESI-QTOF/MS, a total of 148 phenolic compounds were tentatively identified in juniper and hops, among which phenolic acids (including hydroxybenzoic acids, hydroxycinnamic acids and hydroxyphenylpropanoic acids) and flavonoids (mainly anthocyanins, flavones, flavonols, and isoflavonoids) were the main polyphenols, which may contribute to their antioxidant capacity. Furthermore, the HPLC quantitative analysis showed that both samples had a high concentration of phenolic acids and flavonoids. In the HPLC quantification, the predominant phenolic acids in hops and juniper berries were chlorogenic acid (16.48 ± 0.03 mg/g dw) and protocatechuic acid (11.46 ± 0.03 mg/g dw), respectively. The obtained results highlight the importance of hops and juniper berries as a rich source of functional ingredients in different food, beverage, and pharmaceutical industries.