In the present study, the methanolic extracts of Cytisopsis dorycniifolia and Ebenus hirsuta were analyzed for antioxidant, enzyme inhibitory, antimicrobial and antigenotoxic activities. The identification and quantification of phenolic compounds in these extracts were performed using liquid chromatography coupled with mass spectrometry (LC-MS/MS) technique, and the main components were hyperoside, rutin, hesperidin, tannic acid and p-coumaric acid. The extracts had remarkable biological effects. Generally, C. dorycniifolia had higher level of bioactive components and exhibited stronger in vitro antioxidant effects than E. hirsuta. E. hirsuta was active especially against bacteria Pseudomonas fluorescens and Agrobacterium tumefaciens and fungi Puncturella fastigiata, while C. dorycniifolia was active against bacteria E. faecalis and had moderate activity against Trichoderma species. The extracts displayed strong antigenotoxic effects (98.6% for E. hirsuta and 76.3% for C. dorycniifolia). Our findings suggested that C. dorycniifolia and E. hirsuta could be beneficial for the preparation of high-value pharmaceuticals and functional food ingredients.