Stained glass fragments from the 15th, 16th and 20th centuries, belonging to Mosteiro de Santa Maria da Vitória, Batalha (Portugal), were characterised non-destructively in a nuclear microprobe. The work aimed at finding the composition of the glasses and glass paintings and relating these with the corresponding production periods.The elemental compositions of the glass fragments were obtained by means of scanning micro-beam Particle Induced X-ray Emission (μ-PIXE) spectrometry in selected cross-sections. These were complemented by micro X-Ray fluorescence spectrometry. Characterisation of colour was performed by optical absorption spectroscopy in the UV–vis range, while the corrosion products were identified by optical microscopy and μ-FTIR (Fourier Transform Infra Red) spectroscopy in combination with the data generated by μ-PIXE.Nuclear microprobe analysis allowed unveiling the compositions and structures, in particular of glass paintings and corrosion products. While it is not surprising that Fe, Cu and Pb were the main elements identified in the grisaille paintings of all studied periods, as well as Ag and Cu found in the glasses decorated with yellow silver painting, their distribution gave important clues on the materials and techniques used to manufacture these stained glasses. Furthermore, it allowed establishing a definite relation between the compositions found and the periods of production, with the added bonus of correctly reassigning the manufacturing period of some samples.