Antimicrobial resistance genes threaten the effective treatment of infectious diseases, underscoring the importance of their control in line with the EU One Health policy. Wastewater treatment plants are recognized hotspots for antimicrobial resistance. We assessed whether multi-channel mixed-matrix membranes (MCMMMs)—polyethersulfone (PES)/polyvinylpyrrolidone (PVP) ultrafiltration membranes with embedded activated carbon—can concurrently reduce microorganisms and extracellular DNA in wastewater effluent, building on prior reports of micropollutant removal. We evaluated the performance of MCMMMs in removing Escherichia coli and Saccharomyces cerevisiae as model organisms, as well as colony-forming units (CFUs) from wastewater effluent at a transmembrane pressure of 1 bar with a filtration area of 66 cm² over 1 h. DNA was extracted from wastewater effluent following filtration and analyzed to assess changes in microbial community composition. MCMMMs achieved log₁₀ reductions of 5.47 ± 0.42 (Escherichia coli), 5.99 ± 0.46 (Saccharomyces cerevisiae), and 2.79 ± 0.31 (wastewater CFU); reductions by pure PES/PVP membranes were comparable: higher for Escherichia coli and wastewater CFUs, lower for Saccharomyces cerevisiae. Amplicon sequencing showed altered relative abundances in wastewater effluent. Collectively, these findings demonstrate the potential of MCMMMs to simultaneously remove microorganisms, extracellular DNA, and micropollutants, highlighting their suitability for water treatment applications within the One Health framework.