On-chip detection of biological analytes can enable diagnosis at the point of care. Combining the advantages of microelectromechanical system (MEMS) technology and molecular methods, we present the design of an integrated microfluidic platform, a microelectrochemical sensor (mu ECS), and its implementation for the detection of methicillin resistance in Staphylococcus aureus. This platform is capable of electrochemically sensing the target analyte in a microfluidic reactor without the usage of bulky electrodes, rendering it useful for in vitro diagnostics. In our experiments, the functionality of the sensor was tested for detecting specific DNA sequences of mecA gene (an indicator of methicillin resistance) over a range of concentrations of DNA (down to 10 pM). Synthetic oligonucleotides and bacterial PCR product were used as a target analyte in Hoechst 33258 marker-based detection and horseradish peroxidase-based detection, respectively. The results revealed that this platform has high sensitivity and selectivity. Also, its compatibility to MEMS processes enables its use with different applications ranging from detecting various types of cancers to endemics. The designed mu ECS can enable the detection of biological analytes of interest at low cost and high throughput.