We report on the fabrication of a boron-doped nanocrystalline diamond (NCD) 3 × 3 high-density microelectrode array (MEA) for amperometric measurements, with a single electrode area of 3 × 5 μm 2 and a separation in the μm scale. The NCD microelectrodes were grown by hot filament chemical vapor deposition (HFCVD) on a double-side polished sapphire wafer in order to preserve the diamond transparency. Bias enhanced nucleation (BEN) was performed to ensure a covalent adhesion of the films to the substrate. A current background noise of less than 5 pA peak to peak over a 1 kHz bandwidth resulted from an electrochemical investigation of the new device, using 100 mM KCl solutions and ferrocyanide red-ox couples. Cyclic voltammetry measurements in physiological buffer solution and in the presence of oxidizable biomolecules strengthened its suitability for bio-sensing. When compared to a 2 × 2 NCD microelectrode array prototype, already used for in vitro cell measurements, the signal to noise ratio of the amperometric response of the new 3 × 3 device proved twice as good. In addition, the optical transmittance of the boron-doped thin layers exceeded 40% in the visible wavelength range. The excellent electrochemical properties of NCD electrodes and the transparency in combination with the high spatial resolution make the new 3 × 3 NCD MEA a promising tool for electrochemical sensing in a variety of applications, ranging from medical to industrial, in neutral or harsh environments.