Carbamate pesticides are popularly used in agriculture due to their relatively low toxicity and their more degradable nature compared to organophosphates. Resultant residues pose a threat to human and animal health, aquatic systems and wildlife. Carbaryl and thiodicarb are used to control pests in a variety of agricultural crops. Monitoring the level of these pesticides in the environment is crucial in ensuring environmental safety. Multi-template imprinted polymers combined with surface enhanced Raman spectroscopy (SERS) are attractive for sensitive and effective multiple analyte detection for application in pesticide residue studies in environmental matrices. A core–shell Ag-dual template molecularly imprinted polymer (MIP) composite was synthesized and evaluated in this study. Computational design was used to study intermolecular interactions in the pre-polymerization mixture between methylacryamide (MAM) (functional monomer) and the templates carbaryl (CBL) and thiodicarb (TDC). The interaction between the computer simulated template-functional monomer complexes was evaluated by examining the hydrogen bonds to provide insights on the observed binding performance of the dual imprinted polymer. The MIP was then synthesized and its binding properties towards CBL and TDC investigated experimentally. More so, we compared the performance of the mono-template MIP materials and the dual-template MIP material in detection of the templates. The experimental results corroborate the computer simulation results and reveal that CBL has higher adsorption capacity as supported by higher number of hydrogen bonds in the template monomer complex. Therefore, the study presents a cost-effective approach that utilizes a dual-template imprinted polymer for detection of carbamate pesticide residues.