We present a systematic study on the effects of CF4 plasma immersion ion implantation (PIII) in Si on the phase evolution of ultra-thin Ni silicides. For 3 nm Ni, NiSi2 was formed on Si substrates with and without CF4 PIII at temperature as low as 400 °C. For 6 nm Ni, NiSi was formed on pure Si, while epitaxial NiSi2 was obtained on CF4 PIII Si. The incorporation of C and F atoms in the thin epitaxial NiSi2 significantly reduces the layer resistivity. Increasing the Ni thickness to 8 nm results in the formation of NiSi, where the thermal stability of NiSi, the NiSi/Si interface and Schottky contacts are significantly improved with CF4 PIII. We suggest that the interface energy is lowered by the F and C dopants present in the layer and at the interface, leading to phase evolution of the thin Ni silicide.