We present a flexible, polymer based MEMS differential scanning calorimetric (DSC) device combining integrated microfluidic channels, highly sensitive thermoelectric sensing, and real-time temperature monitoring for thermodynamic characterization of biomolecular samples with minimized sample consumption. The device uses an inexpensive, commercially available polymer substrate and a novel fabrication approach to create a microstructure consisting of a pair of microchannels (containing the sample and reference buffer, respectively), which are integrated with resistive temperature sensors (for in-situ measurement of sample temperature) and an antimony-bismuth (Sb-Bi) thermopile (for measurement of the temperature difference between the sample and reference channels). We demonstrate the utility of this MEMS DSC device by measuring the unfolding of lysozyme in a small volume (1 μL), and at practically relevant protein concentrations (approaching 1 mg/mL). Thermodynamic properties including the total enthalpy change per mole of protein (ΔH) and melting temperature (Tm) at different protein concentrations during this conformational transition are determined and found to agree with published data.