The restoration of the four northern windows of the 13th century Sainte-Chapelle in Paris from 2011 to 2014 has offered a unique opportunity to investigate the chemical composition and color of medieval glasses. This impressive corpus, covering a total surface of 660 m2, was created in a record time of a few years. The glasses from ten selected panels were analyzed using non-destructive and non-invasive techniques, with a specific consideration for the color of the glasses. Ion beam analyses performed at the New AGLAE facility enabled revealing that all ancient glasses are “potash” type glasses made from plant ashes, likely beech, in agreement with previous results on off-site panels. The multivariate analysis of major and minor elements demonstrates the presence of compositional clusters with a small variability suggesting the identification of bundles of glasses. The coloration of the glasses was measured by optical absorption spectroscopy, using a mobile spectrophotometer over the entire UV–visible-NIR energy range. The color palette is made of six colors assigned to typical medieval recipes. The chromophores of the different glasses are identified by combining the chemical composition, optical absorption spectroscopy and colorimetry. Colorless, yellow and purple glasses arise from the subtle redox equilibrium between manganese and iron. Their reduced usage shows their uncertain production. Blue glasses are colored by Co2+ using saffre from the contemporary German mines, green glasses are colored by Cu2+ and Fe3+ using high concentrations of copper and red glasses are striated glass colored by metallic copper nano-particles. Glass matrix and chromophores form compositional clusters, which are spread among the panels of the four windows suggesting that the glazing of these four windows was run simultaneously by the same atelier using the same supply of glass.