The data set consists of the raw and analysis data. Positron annihilation lifetime spectroscopy depth profiles were measured at the positron ELBE during the PI beamtime on November 2023 (POS23203233). MBE deposited Ge layers at temperatures of 100°C - 350°C have been evaluated concerning defect microstructure. The most dominant defect, namely Ge vacancy, has been evidenced independently on the temperature conditions. The results support the main claim of the manuscript, feasibility of the low temperature growth approach to Ge.