Phenolic compounds, naturally present in plants, are particularly relevant as nutraceutics for their antioxidant activities. Here, choline chloride-based natural deep eutectic solvents (NaDESs) were used for efficient extraction of total phenolic compounds (TPC) from leaves, pods and roots of Rhamnus alaternus plant. In each extract, the polyphenols content and their antioxidant activities were evaluated. More, their antibacterial activity was carried out against Gram-positive and Gram-negative bacteria. The investigated extracts presented antioxidant and antimicrobial activities. The leaves, pods and roots extracts obtained using the choline chloride-glycerol (ChCl-Gly) mixture exhibited a high value of TPC comprised within 437.7 and 317.0 mg GAE/100 g d.w. and showed the best antioxidant properties with ABTS radical scavenging capacity (IC50: from 44.55 to 53.56 µg/mL), DPPH assay (IC50: from 26.36 to 118.23 µg/mL), reducing activity (EC50: from 77.53 to 85.05 µg/mL) and iron chelation activity (EC50: from 91.73 to 108.7 µg/mL). In contrast, choline chloride-urea (ChCl-Ur) extracts showed a low antioxidant capacity. Lastly, the best bioactive extracts were characterized using HPLC-MS/MS to determine their bioactive compounds. The present study suggests that the DES-based method developed was selective, efficient and sustainable for extraction of polyphenols.