In this study, we aimed to compare the phytochemical compounds (polyphenols and flavonoids), antioxidant activity, functional groups present in the compounds (FTIR), and anti-microbial effects, in aqueous and methanol extracts obtained from flowers of commercial Hypericum perforatum and native Papaver Rhoeas from Morocco. P. Rhoeas L was collected from El Lhaj Kaddour near Meknes, while H. perforatum L was bought in a dried state from a Moroccan herbalist in the same city. Total polyphenols were evaluated using the Folin-Ciocalteu reagent, respectively. The antioxidant activity was assessed via DPPH and anti-microbial effects were tested against six bacteria (Gram- and Gram+). In aqueous and methanol extracts of P. Rhoeas had the highest TPC value (23.67 ± 0.94 mg GAE/g; 15.86 ± 0.65 mg GAE/g) compared to H. perforatum (15.26 ± 1.30 mg GAE/g; 5.50 ± 1.13 GAE/g). The aqueous extract of Papaver Rhoeas exhibited the highest TFC at 14.36 ± 0.49 mg QE/g, while the methanol extract of Hypericum perforatum had the highest 10.65 ± 0.49 mg QE/g in TFC. In contrast, methanol and aqueous extracts of H. perforatum showed significant zones of inhibition against Staphylococcus aureus (9.5 ± 0.5 mm and 10.17 ± 0.29 mm) and Staphylococcus epidermidis (8.33 ± 0.58 mm and 9.33 ± 0.58 mm) respectively, with a minimum inhibitory concentration was estimated at 10 µL/ml. The FTIR analysis demonstrated that the extracts of both plants are rich in bioactive molecules with potential biological activities and a pharmaceutical industry perspective. Consequently, these Papaver Rhoeas and Hypericum perforatum extracts exhibit antioxidant and antibacterial activities.