Iron gall inks have been among the most used writing materials after carbon black, thus representing an important element of the historical and artistic heritage of our society. Crucially, the preservation of manuscripts and drawings is influenced by the presence of these inks, leading to conservation issues related to paper degradation and text fading. Besides all the advances obtained in paper conservation, the study of iron gall ink’s behaviour and ageing is still an important topic, which requires investigation through an accurate molecular characterisation to produce reliable models. In the present work a micro-destructive method based on liquid chromatography techniques (HPLC-DAD and HPLC-ESI-Q-ToF) has been optimised starting from a model gallic acid-based ink. An in-depth study of the behaviour of the ink in time was performed by natural and artificial ageing tests, monitored by colorimetry, showing the autoxidation of gallic acid to ellagic acid in the prepared mock-ups. The effect of relative humidity on ageing processes was also evaluated, allowing us to determine different intermediates depending on the environmental conditions. Finally, the analytical method developed was then successfully applied for investigating 19th–20th century historical ink samples, where one of the identified ageing markers was detected, besides the expected gallic and ellagic acids.