The Basilica di Santa Croce is the major Franciscan church in Florence. Among the prominent masterpieces preserved in this church are 22 medieval stained glass windows. Between 2000-2013,the Opera di Santo Croce started a restoration campaign of six of the most important ones, dated 14th century. In this paper the archaeometric data collected during the restoration campaign are reported. Two major base glass compositions (potash-lime-silica and soda-lime-silica) were identified by quantitative chemical analysis. Results are compared with similar investigations on Italian stained glass windows of the 14-15th centuries and many similarities are highlighted. Some interesting secrets of the colouring techniques based also on multilayer glass pieces were revealed. Finally, SEM-EDS analyses allowed the main weathering glass phenomena to be investigated.