Electroanalytical methods are increasingly used in the understanding of the complexity of the human brain function in normal and diseased states. The main component of the electroanalytical methods is an electrode and its electrochemical properties are linked to the overall performance of the sensor used in detecting the various electroactive brain chemicals and molecules. In this work, we developed a droplet-based microfluidic platform and characterized a boron-doped ultrananocrystalline diamond (BDUNCD) microelectrode that is modified with multi-walled carbon nanotubes (MWCNTs) thin film and nafion coatings. The coating parameters were systematically altered and studied their effect on dopamine (DA) sensing performance. BDUNCD microelectrodes that were modified with 50 nm thick nafion coating showed a 3-fold increase in DA detection signal, whereas the microelectrodes modified with MWCNT film and nafion coating showed a 10-fold increase in the detection signal. The un-modified and modified BDUNCD microelectrodes were evaluated for their long-term stability (up to 9 h) using a custom droplet-based microfluidics. The MWCNT-nafion modified BDUNCD microelectrode showed the highest sensitivity of 15.01 μA ± 0.2% for 100 μM DA concentration with a limit of detection of 1.78 nM ± 2%.