Abstract: The speed and effectiveness of a conservation treatment used for stained glass windows have been investigated. Dark-coloured Mn-rich stains can be found in the alteration layer of ancient glass artefacts and cause the surface to turn brown/black: this phenomenon is known as Mn-browning or Mn-staining. While in glass manganese is present in the +II or +III oxidation states, in the Mn-rich bodies, manganese is in a higher oxidation state (+IV). In restoration practice, mildly reducing solutions are employed to eliminate the dark colour and restore the clear appearance of the glass. In this paper the effectiveness and side effects of the use of hydroxylamine hydrochloride for this purpose are assessed. Archaeological fragments of stained glass windows, dated to the 14th century and originating from Sidney Sussex College, Cambridge (UK), were examined by means of synchrotron radiation (SR) based microscopic X-ray Absorption Near-Edge Spectroscopy (μ-XANES) and microscopic X-Ray Fluorescence (μ-XRF) and with high resolution computed absorption tomography (μ-CT) before, during and after the treatment. The monitoring of the glass fragments during the treatment allows us to better understand the manner in which the process unfolds and its kinetics. The results obtained reveal that the hydroxylamine hydrochloride treatment is effective, but also that it has a number of unwanted side effects. These findings are useful for optimizing the time and other modalities of the Mn-reducing treatment as well as minimizing its unwanted results.