Background/Objectives: This study investigates the development of 3D chitosan-x-cobalt ferrite scaffolds (x = 5, 7.5, and 10 wt%) with interconnected porosity for potential biomedical applications. The objective was to evaluate the effects of magnetic particle incorporation on the scaffolds’ structural, mechanical, magnetic, and biological properties, specifically focusing on their biocompatibility and antimicrobial performance. Methods: Scaffolds were synthesized using freeze-drying, while cobalt ferrite nanoparticles were produced via a pilot-scale combustion reaction. The scaffolds were characterized for their physical and chemical properties, including porosity, swelling, and mechanical strength. Hydrophilicity was assessed through contact angle measurements. Antimicrobial efficacy was evaluated using time kill kinetics and agar diffusion assays, and biocompatibility was confirmed through cytotoxicity tests. Results: The incorporation of cobalt ferrite increased magnetic responsiveness, altered porosity profiles, and influenced swelling, biodegradation, and compressive strength, with a maximum value of 87 kPa at 7.5 wt% ferrite content. The scaffolds maintained non-toxicity and demonstrated bactericidal activity. The optimal concentration for achieving a balance between structural integrity and biological performance was found at 7.5 wt% cobalt ferrite. Conclusions: These findings suggest that magnetic chitosan-cobalt ferrite scaffolds possess significant potential for use in biomedical applications, including tissue regeneration and advanced healing therapies. The incorporation of magnetic properties enhances both the structural and biological functionalities, presenting promising opportunities for innovative therapeutic approaches in reconstructive procedures.