Abstract Since the recent development of a mobile setup, MA-XRF scanning proved a valuable tool for the non-invasive, technical study of paintings. In this work, the applicability of MA-XRF scanning for investigating stained-glass windows inside a conservation studio is assessed by analysis of a high-profile, well-studied late-mediaeval panel. Although accurate quantification of components is not feasible with this analytical imaging technique, plotting the detected intensities of K versus Ca in a scatter plot allowed distinguishing glass fragments of different compositional types within the same panel. In particular, clusters in the Ca/K correlation plot revealed the presence of two subtypes of potash glass and three subtypes of high lime low alkali glass. MA-XRF results proved consistent with previous quantitative SEM-EDX analysis on two samples and analytical-based theories on glass production in the Low Countries formulated in literature. A bi-plot of the intensities of the more energetic Rb–K versus Sr–K emission lines yielded a similar glass type differentiation and is here presented as suitable alternative in case the Ca/K signal ratio is affected by superimposed weathering crusts. Apart from identification of the chromophores responsible for the green, blue and red glass colors, contrasting the associated elemental distribution maps obtained on the exterior and interior side of the glass permitted discriminating between colored pot metal glass and multi-layered flashed glass as well. Finally, the benefit of obtaining compositional information from the entire surface, as opposed to point analysis, was illustrated by the discovery of what appears to be a green cobalt glass—a feature that was previously missed on this well-studied stained-glass window, both by connoisseurs and spectroscopic sample analysis.