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The possibility of modifying the surface chemistry of materials and synthetizing inorganic particles in natural aqueous extracts of plants (avoiding calcination), opens the doors to undoubtedly interesting scenarios for innovative functionalization strategies that are increasingly eco-sustainable and rich in interesting chemical–physical and biochemical properties. Among the aerial plants, Satureja montana exhibits interesting antibacterial, antifungal, antimicrobial, and antioxidant activities due to the rich volatile and non-volatile compounds (characterized by gas chromatography–mass spectrometry), contained in the aqueous extracts. For the first time, the latter was applied for the green synthesis of TiO2 and CaCO3 particles, characterized by X-ray diffraction, Raman, infrared spectroscopies, and scanning electron microscopy, coupled with microanalysis. Screening through antimicrobial assays under indoor passive sedimentation conditions showed opposite trends for two kinds of particles. TiO2 anatase spherical particles (400 < φ < 600 nm) increase microbial growth, proportionally to increasing particle concentration. Instead, S. montana-functionalized CaCO3 prismatic microparticles (1 µm × 1 µm × 1 µm) exhibit strong and dose-dependent antimicrobial activities, achieving near-complete inhibition at 50 mg/mL.