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Preparation and characterization of CS/Fe3O4/CMC composite scaffolds including the morphology, crystallinity, and the in vitro efficacy as antibiotic delivery vehicles as well as their influence on the eukaryotic cells are reported. The results demonstrated that the magnetic polymeric composite scaffolds are exhibiting structural and functional properties that recommend them for further applications in the biomedical field. They improve the activity of currently used antibiotics belonging to penicillins, macrolides, aminoglycosides, rifampicines and quinolones classes, representing potential macromolecular carriers for these antimicrobial substances, to achieve extracellular and intracellular targets. The obtained systems are not cytotoxic and do not influence the eukaryotic HCT8 cell cycle, representing potential tools for the delivery of drugs in a safe, effective and less expensive manner.