The process of bonding to dentin is complex and dynamic, greatly impacting the longevity of dental restorations. The tooth/dental material interface is degraded by bacterial acids, matrix metalloproteinases (MMPs), and hydrolysis. As a result, bonded dental restorations face reduced longevity due to adhesive interfacial breakdown, leading to leakage, tooth pain, recurrent caries, and costly restoration replacements. To address this issue, we synthesized and characterized a multifunctional magnetic platform, CHX@SiQuac@Fe3O4@m-SiO2, to provide several beneficial functions. The platform comprises Fe3O4 microparticles and chlorhexidine (CHX) encapsulated within mesoporous silica, which was silanized by an antibacterial quaternary ammonium silane (SiQuac). This platform simultaneously targets bacterial inhibition, stability of the hybrid layer, and enhanced filler infiltration by magnetic motion. Comprehensive experiments include X-ray diffraction, FT-IR, VSM, EDS, N2 adsorption-desorption (BET), transmission electron microscopy, scanning electron microscopy, thermogravimetric analysis, and UV-vis spectroscopy. Then, CHX@SiQuac@Fe3O4@m-SiO2 was incorporated into an experimental adhesive resin for dental bonding restorations, followed by immediate and long-term antibacterial assessment, cytotoxicity evaluation, and mechanical and bonding performance. The results confirmed the multifunctional nature of CHX@SiQuac@Fe3O4@m-SiO2. This work outlined a roadmap for (1) designing and tuning an adhesive formulation containing the new platform CHX@SiQuac@Fe3O4@m-SiO2; (2) assessing microtensile bond strength to dentin using a clinically relevant model of simulated hydrostatic pulpal pressure; and (3) investigating the antibacterial outcome performance of the particles when embedded into the formulated adhesives over time. The results showed that at 4 wt % of CHX@SiQuac@Fe3O4@m-SiO2-doped adhesive under the guided magnetic field, the bond strength increased by 28%. CHX@SiQuac@Fe3O4@m-SiO2 enhanced dentin adhesion in the magnetic guide bonding process without altering adhesive properties or causing cytotoxicity. This finding presents a promising method for strengthening the tooth/dental material interface's stability and extending the bonded restorations' lifespan.