MA-XRF is a novel macroscopic imaging technique originally developed for easel paintings and recently made available to glass conservators. This paper discusses the first real-life contribution of MA-XRF imaging to a conservation intervention of stained-glass panels. The six panels under study belong to the cathedral building since their creation in 1555–1559 AD. MA-XRF appeared an outstanding tool for first-line screening of stained-glass windows, providing readily interpretable information on glass type, coloring and alteration processes. In particular, the chemical imaging technique allowed distinguishing unambiguously the surviving original glass panes from later additions, thereby ensuring a correct historical understanding. From a more practical point of view, the experiments supplied accurate schemes that can be directly incorporated in condition reports and assist designing the ensuing conservation approach.