The research question that is addressed in this paper relates to the performance limitations of thermal flow sensors due to miniaturization. Sensor elements in current microflow sensors are mostly made by metal thin films. The problem is that thin-films reproduce poorly and that practically all material properties are subject to drift. This drift and poor reproducibility translates directly into the accuracy of thermal microflow sensors. This paper presents a thermal flow sensor consisting of freely suspended silicon-rich silicon-nitride microchannels with an integrated Al/poly-Si++ thermopile in combination with up and downstream Al heater resistors. The drift-free zero offset of a thermopile at uniform temperature is exploited in a feedback loop controlling the dissipated powers in Al heater resistors, reducing inevitable influences of resistance drift, and mismatch of thin-film metal resistors. The control system attempts to cancel the flow-induced temperature imbalance across the thermopile by controlling a power difference between both heater resistors, thereby giving a measure of the flow rate nearly independent of material drift.