This paper presents a method with an accurate control of threshold voltages (Vth) of AlGaN/GaN high-electron mobility transistors (HEMTs) using a fluoride-based plasma treatment. Using this method, the Vth of AlGaN/GaN HEMTs can be continuously shifted from −4 V in a conventional depletion-mode (D-mode) AlGaN/GaN HEMT to 0.9 V in an enhancement-mode AlGaN/GaN HEMT. It was found that the plasma-induced damages result in a mobility degradation of two-dimensional electron gas. The damages can be repaired and the mobility can be recovered by a post-gate annealing step at 400 ◦C. At the same time, the shift in Vth shows a good thermal stability and is not affected by the post-gate annealing. The enhancement-mode HEMTs show a performance (transconductance, cutoff frequencies) comparable to the D-mode HEMTs. Experimental results confirm that the threshold-voltage shift originates from the incorporation of F ions in the AlGaN barrier. In addition, the fluoride-based plasma treatment was also found to be effective in lowering the gate-leakage current, in both forward and reverse bias regions. A physical model of the threshold voltage is proposed to explain the effects of the fluoride-based plasma treatment on AlGaN/GaN HEMTs.