Cistaceae is a large family of shrubs commonly distributed in the Mediterranean ecosystem. The aim of this study was to explore the potential antimicrobial properties against E. coli and/or S. aureus of different extracts obtained from four Cistaceae species that are especially abundant in Spanish semi-arid regions. MIC(50) values of the extracts of C. salviifolius exhibited potent bacteriostatic effects against S. aureus compared with the other Cistus species tested. Spray-drying had less impact on the antimicrobial activities and polyphenolic contents than did evaporation followed by freeze-drying. When C. salviifolius extract was concentrated and the polar fraction was removed, its bacteriostatic and bactericidal activities against both strains were significantly enhanced. Seasonal influences on the composition have also been found. Up to forty-eight compounds were found in the aqueous extract of C. salviifolius using RRLC-ESI-TOF-MS. The analysis of the composition of the extracts revealed that the inhibitory activity against E. coli may be related to the presence of galloylated flavanols and specific flavonols, whereas the inhibitory capacity against S. aureus may be related primarily to polar compounds and to other flavonols. Potential synergistic effects among polyphenols may deserve further studies. These extracts may serve as an alternative source of antimicrobial ingredients focused on medical devices or cosmetics.