We study effects of low temperature hydrogen plasma treatment (200 – 300 °C) done in two different microwave plasma reactors (linear and focused plasma) on functionality of diamond solution-gated field-effect transistors (FET) covered with various encapsulation (ma-P, OFPR, SU8, Si 3 N 4) and with proteins adsorbed on the gate. Three-dimensional transistor microstructures (20 μm) are made of nanocrystalline hydrogen terminated intrinsic diamond that is grown on Si/SiO 2 substrates by selective seeding and microwave plasma CVD growth. The hydrogen-plasma treatment in linear plasma system at 200 °C removes the proteins from the gate as evidenced by atomic force microscopy, keeps the FET fully operational, and renews solution-gated FET sensitivity to protein adsorption (unlike rinsing in solutions) as evidenced by reproducible shift of transfer characteristics by -30 mV. At the same time, due to larger distance (7 cm) from the high-density plasma region this process enables to preserve the polymer-based encapsulation, unlike to more aggressive treatment in focused plasma.