Old manuscripts are among the most important elements of the cultural and historical heritage of ancient knowledge. Unfortunately, many of them suffer from degradation, mostly those written with iron gall inks. In the present work, a study using non-destructive techniques was designed with the aim of analyzing the elemental composition and structural characteristics of iron gall inks, reproduced in laboratory, paper and their interaction when the ink is deposited on paper, inducing the paper degradation. Proton induced X-ray emission, X-ray diffraction and Fourier-transform infrared spectroscopy provided the elemental and structural information, and photography under infrared (IR) and ultraviolet (UV) light allowed the differentiation between manufactured inks. Results show that the first step of inked paper deterioration is due to acid-hydrolysis of the cellulose and the presence of reactive Fe(II) species by reducing the crystallinity index of the paper, which is affected depending on the ink recipe and the starting raw materials. These results will be useful to future studies on ancient documents written with iron gall inks, which suffer deterioration due to ink corrosion, and to differentiate between the different paper degradation mechanisms.