We present hydrogenated amorphous silicon (a-Si:H) films which were deposited on two different substrates (glass and mono-crystalline silicon) after an isothermal annealing treatment at 250 ◦C for up to 14 h. The annealed amorphous films were analyzed using atomic force microscopy, Raman and FTIR spectroscopy. Films deposited on glass substrate experienced an amorphous–crystalline phase transition after annealing because of the metal-induced crystallization effect, reaching approximately 70% conversion after 14 h of annealing. An absorption frequency of the TO-phonon mode that varies systematically with the substoichiometry of the silicon oxide in the 1046–1170cm−1 region was observed, revealing the reactivity of the film with the annealing time. For similar annealing time, films deposited on mono-crystalline silicon substrate remained mainly amorphous with minimal Si-crystalline formation. Therefore, the crystalline formations and the shape of the films surfaces depends on the annealing time as well as on the substrate employed during the deposition process of the a-Si:H film.