Barium di-silicide (BaSi2) is a very promising absorber material for high-efficiency thin-film solar cells, due to its suitable bandgap, high light absorption coefficient, and long minority-carrier lifetime. In this study, we compare the nanostructure, layer composition, and point defects of BaSi2 thin films deposited by Radio Frequency (RF) sputtering, Thermal Evaporation (TE), and Molecular Beam Epitaxy (MBE), using Doppler Broadening Positron Annihilation Spectroscopy (DB-PAS) depth profiling, Raman spectroscopy, and x-ray diffraction. Our DB-PAS study on thermally annealed RF-sputter deposited and on TE-deposited BaSi2 layers, in a comparison with high quality BaSi2 films produced by MBE, points to the presence of vacancy-oxygen complexes and Si or Ba mono-vacancies, respectively, in the (poly)crystalline BaSi2 films. The degree of near-surface oxidation increases, going from MBE and TE to the industrially applicable RF-sputtered deposition synthesis. The use of a-Si capping layers on the thermally annealed RF-sputtered BaSi2 films leads to a clear reduction in sub-surface oxidation and improves the quality of the BaSi2 films, as judged from DB-PAS.