This paper reports the study of corrosion in two stained glass panels from the south aisle of Sta. Maria da Vitória monastery, at Batalha (Portugal), one depicting the Last Supper (dated from 1508), and the other one showing a saint (c. 1450). These panels exhibit extensive corrosion with darkening phenomena that are an impediment to their correct visualization, a source of major concern both to conservators and curators. By using external micro-beam Particle Induced X-ray Emission (PIXE) and Particle Induced Gamma Emission (PIGE) spectrometry, the elemental compositions of large fragments were obtained, enabling the selection of representative corroded areas, from which elemental distribution maps were produced by scanning. Calcium and potassium rich structures were found – at the surface and inside cavities in the glass – that were identified as oxalates and carbonates, by Raman microscopy and micro-FTIR. The dark spots present in the glass surfaces were found to be Zn and Pb rich.These findings indicate that the corrosion observed was due not only to reactions with atmospheric water and CO2 but also with the oxalic acid secreted by micro-organisms. Furthermore, it did not result from reactions with atmospheric SO2 or acid rain. The information obtained is relevant for a better understanding of the corrosion processes and products formed on the surface of these panels and therefore for the proper planning of much needed adequate conservation–restoration actions and appropriate display conditions.