This study aimed to assess the effect of high pressure (300 and 600 MPa) and enzymatic extraction (pectinase and cellulase) on the phenolic compounds profile, antioxidant capacity and antimicrobial activity of extracts from pomegranate by-products. Antimicrobial activity against eight different strains of pathogenic and contaminant bacteria and against five beneficial bacteria including Lactobacillus and Bifidobacterium strains were determined. The maximum level of total phenolic content, as well as antioxidant capacity were observed at 300 MPa, however enzymatic extraction did not improve the extraction yields. Punicalagin isomers and bis-hexahydroxydiphenoyl-glucoside isomer were the most abundant phenolic compounds found in the extracts. All pomegranate peel extracts demonstrated selective antimicrobial activity against all pathogenic bacteria without affecting beneficial ones. Pressurized extracts presented lower minimum inhibitory concentration against Bacillus cereus and Pseudomonas aeruginosa and lower minimum bactericidal concentration against B. cereus, while, enzymatic extracts presented lower minimum bactericidal concentration for Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus and Listeria monocytogenes. Principal component analyses reveled that antioxidant activity and phenolic compounds content were strongly related with antimicrobial activity. Pomegranate peels extracts obtained by high pressure extraction could so be used as a source of high added-value bioactive compounds for antioxidant and antimicrobial applications.