Implantable electrochemical sensors enable fast and sensitive detection of analytes in biological tissue, but are hampered by bio-foulant attack and are unable to be recalibrated in-situ. Herein, an electrochemical sensor integrated into ultra-low flow (nL/min) silicon microfluidic channels for protection from foulants and in-situ calibration is demonstrated. The small footprint (5 µm radius channel cross-section) of the device allows its integration into implantable sampling probes for monitoring chemical concentrations in biological tissues. The device is designed for fast scan cyclic voltammetry (FSCV) in the thin-layer regime when analyte depletion at the electrode is efficiently compensated by microfluidic flow. A 3X enhancement of faradaic peak currents is observed due to the increased flux of analytes towards the electrodes. Numerical analysis of in-channel analyte concentration confirmed near complete electrolysis in the thin-layer regime below 10 nL/min. The manufacturing approach is highly scalable and reproducible as it utilizes standard silicon microfabrication technologies.