Regulatory agencies have identified zineb (ZNB) as a potential health hazard due to its toxicological profile and environmental persistence. Therefore, establishing a highly selective and ultrasensitive method for ZNB detection is crucial for environmental monitoring, food safety assurance, and effective pesticide regulation enforcement. Herein, a selective electrochemical sensor was engineered based on a molecularly-imprinted polymer (MIP) film designed for targeted analyte recognition. The sensing platform integrates bimetallic cobalt–manganese metal–organic frameworks (CoMn-MOFs) with reduced graphene oxide (rGO) to enhance conductivity and surface activity. Initially, GO was synthesized and subsequently reduced to conductive rGO utilizing sodium borohydride via a modified Hummers’ method, forming a high-conductivity matrix for efficient electron transfer. Second, CoMn-MOFs were incorporated to significantly enhance the active surface area and facilitate electron transfer. A selective MIP layer was formed on the electrode surface via electro-polymerization, enabling precise molecular recognition of ZNB. The resulting MIP/rGO/CoMn-MOFs-modified glassy carbon electrode (GCE) exhibited excellent analytical performance, including a broad linear range (0.01–200 nM), a low LOD (4.0 pM), and high selectivity against potential interferents. When applied to real food and water samples, the sensor achieved high accuracy, with recoveries  ranging from 95.5% to 105.6% and RSDs between 1.87% and 4.00%. The method was validated using the standard addition technique, confirming its applicability for accurate ZNB quantification in complex food and water matrices. These findings validate the sensor’s potential as a practical, rapid, and environmentally friendly platform for monitoring ZNB residues in agricultural and environmental contexts.