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This work presents a fully-functional, microfabricated electrochemical-cantilever hybrid platform with flow control. A new cantilever chip format is designed, fabricated, and mounted in a custom polymer flow cell. Issues such as leakage and optical/electrical access are addressed, and combined mechanical and electrochemical performance is investigated. Lastly, a cantilever is “defunctionalized” in situ to create a reference cantilever for differential measurements in detection of Cu2+ ions at concentrations of 10 μM and 100 nM.