In this paper, a comparative study of C-, N- and Xe-based pre-amorphization implantation (PAI) processes is proposed. The impact of the use of such processes on the agglomeration resistance and physical properties of the final Ni(Pt)Si layer, as well as the formation mechanisms via solid-state reactions and electrical performances via the transfer length measurement (TLM) method, is evaluated. It is shown that although all species are able to increase the agglomeration temperature of Ni(Pt)Si layers (up to more than 100 °C), the underlying mechanisms are different. For C- and N-based PAI processes a strong chemical effect is observed, while for Xe-based processes the amorphization depth plays an important role. Consequently, the beneficial effect of stabilizing Ni(Pt)Si layers at high temperatures using C- and N-based PAI processes has to be balanced with an increased layer resistivity (up to 30%) combined with a strong deterioration of the associated specific contact resistivity (which is multiplied by almost a factor 10). In this sense, Xe-based PAI processes seem to be a better option as they could allow to combine both requirements.