A masterpiece of European Art Nouveau and one of the greatest sets of stained glass windows in modern world art. In 1895, Mehoffer's design, which was young and unknown outside Kraków (a carton of stained-glass Apostles), won an international competition for which 47 designs were submitted. By 1934, Mehoffer's stained glass windows filled the remaining large windows of the side aisles and the presbytery (13 windows in total), creating a Gothic cathedral decoration ensemble unique in modern art. The painter was encouraged to send his design to Freiburg by Tadeusz Stryjeński, with whom he had collaborated on the decoration of St Mary's Church in Kraków, and who knew about the competition thanks to his family connections to Freiburg.

The stained glass windows fill most of the cathedral's large windows (except for the upper storey and the Chapel of the Holy Sepulchre), determining its programme and the aesthetic value of the interior. At the same time, they show the evolution of Mehoffer's work, from the decorative patterns of his master Jan Matejko in the polychrome of St Mary's Church in Krakow, through the lush Art Nouveau style, to almost Expressionist scenes. In addition to religious representations (the best of which are the scenes from the stained glass Martyrs: with Sts. Sebastian, Maurice, Barbara and Catherine, 1899, awarded at the World Exhibition in Paris 1900; the Three Kings with Herod's infernal "predella", 1904), the iconography refers to Swiss history and the founding events of the Confederation in the late Middle Ages, bringing out the significance of Freiburg itself (the Battle of Morat, scenes from the life of Bl. Nicholas of Flue, 'Secular Freiburg, Ecclesiastical Freiburg'). The earliest of the whole ensemble are the large windows of the chancel, designed from 1918 and realised until 1934. The artist was able to benefit from the consultation of the members of the jury, as well as from the advice and support given in the following years by, among others, the Dominican Father Joachim Berthier, a professor appointed just before the competition was announced by the University of Freiburg, or one of the best-known art critics in Switzerland, William Ritter.

Mehoffer boldly broke many of the rules that were in force in stained glass in the 19th century, for example, by dynamising his compositions, he allowed scenes or figures to 'move' from one section to another, or even from one window to the plane of the neighbouring window. The compositional concepts were also changing, which makes the whole not monotonous; we are dealing with a living painting story.

Mehoffer produced designs in a scale of 1:5 (most of which have survived), followed by execution sheets in a scale of 1:1 (all of which have survived). The stained glass windows were made at the Kirsch-Fleckner Atelier in Freiburg, which became famous for this work; some windows were made under the artist's personal supervision. They influenced Swiss decorative art, especially the stained glass work of Alexandre Cingria. They were appreciated, among others, by the greatest Swiss artist, Ferdinand Hodler, who was clearly inspired by Mehoffer's painterly work in some of his stained glass windows with historical scenes. The critic Marc de Munnynck wrote:

"There is only one thing one can accuse this work of being too powerful. Its qualities are so evocative, it touches strings so subtle in our souls, it awakens resonances so full of vitality (...) that it becomes painful".

The popularity of Mehoffer's work won him several more smaller private commissions in the region, including for the church in Onnens (1902-1906) and the chateau chapel in Chenaleyres (1908). Research on the Freiburg stained glass ensemble was carried out at the Swiss Vitrocentre in Romont.