Acetamiprid (ACE) and thiacloprid (THIA) are the dominant cyano-substituted neonicotinoids detected in fruit juices and bottled water, which raises food-safety concerns and regulatory scrutiny. Conventional purification with activated carbon or advanced oxidation shows limited selectivity and has a high energy demand. Covalent organic frameworks (COFs) offer tunable chemistry for targeted adsorption, yet no strategy exists to engineer COF sites that preferentially recognize the cyano group of ACE/THIA. Here, we synthesized a magnetic core-shell adsorbent, Fe₃O₄@COF(TBTD-BD)-Au, by growing cyano-affinitive Au nanoparticles on a Cl-decorated COF shell surrounding a Fe₃O₄ core. Under optimized conditions (pH 6.0, 25 °C), the Fe₃O₄@COF(TBTD-BD)-Au achieved maximum adsorption capacities of 157 mg g⁻¹ (ACE) and 156 mg g⁻¹ (THIA). Uptake followed pseudo-second-order kinetics and the Freundlich isotherm; thermodynamic analysis confirmed an endothermic, spontaneous process. Competitive tests showed >80% removal of ACE and THIA in the presence of four co-occurring neonicotinoids, and the adsorbent retained 91.5% of its initial capacity after six adsorption–desorption cycles. Synergistic Au-cyano coordination, Cl-mediated hydrogen bonding, and π–π stacking confinement confer high selectivity and capacity. This ligand-guided, post-functionalized COF provides promising potential in the field of food sample treatment for contaminant removal.