An embedded epitaxial semiconductor portion having a different composition than matrix of the semiconductor substrate is formed with a lattice mismatch and epitaxial alignment with the matrix of the semiconductor substrate. The temperature of subsequent ion implantation steps is manipulated depending on the amorphizing or non-amorphizing nature of the ion implantation process. For a non-amorphizing ion implantation process, the ion implantation processing step is performed at an elevated temperature, i.e., a temperature greater than nominal room temperature range. For an amorphizing ion implantation process, the ion implantation processing step is performed at nominal room temperature range or a temperature lower than nominal room temperature range. By manipulating the temperature of ion implantation, the loss of strain in a strained semiconductor alloy material is minimized.