Aim: Investigating molecularly imprinted polymers (MIPs) in electrochemical biosensors for thrombin detection, an essential protein biomarker. Comparing different monomers to showcase distinct sensitivity, specificity and stability advantages. Materials & methods: Dopamine, thionine and ethanolamine serve as monomers for MIP synthesis. Electrochemical methods and atomic force microscopy characterize sensor surfaces. Performance is evaluated, emphasizing monomer-specific electrochemical responses. Results: Monomer-specific electrochemical responses highlight dopamine's superior signal change and stability over 30 days. Notably, a low 5 pg/ml limit of detection, a broad linear range (5–200 pg/ml) and enhanced selectivity against interferents are observed. Conclusion: Dopamine-based MIPs show promise for high-performance electrochemical thrombin biosensors, suggesting significant applications in clinical diagnostics.