The understanding of the connection between the value of an image and the value of the materials that were used to make it is limited, especially for stained-glass windows. However, such information can bring-to-light how artistic and economic questions were intertwined and how the final artwork depended on the ranking of the materials. With this paper, we aim to illustrate the benefit of combining art historical research with scientific analysis to retrieve the selection of the quality of the materials of stained-glass windows. Therefore, the main objective of this paper is to investigate the link between the materials and the iconography in order to recover artistic choices and highlight a possible hidden symbolism for a set of window panels, used as a first case-study. Glass quality is investigated according to the following parameters: (1) the glass composition, (2) the glass forming technique, (3) the transparency and hue of the colourless glass, and (4) the rarity and complexity of the colouring technology. The results of our research indicate that the four-studied panels were originally assembled from two different glass compositional groups, K-rich glass and Ca-rich glass, and that specific attention was paid to select only high-quality materials and production techniques for the representation of the characters with higher positions in the religious hierarchy. A very interesting aspect concerns the way the bishop was rendered in one of the panels, because it seems that he actually upgraded his own prestige by requesting the use of specific materials and more attentiveness to his rendering in the panel. By this research, we proposed a first case-study with a non-destructive tool to bring a discussion on the use of different glass qualities in stained glass window. We hope to further encourage such studies on window panels across Western Europe to verify if similar observations can be made.