In 1895, Mehoffer was spectacularly successful, winning a competition to create stained glass windows for the collegiate church (later the cathedral) in Freiburg. For the next more than 30 years he created further elements of this grand decoration, becoming an authority in Switzerland and a model for local artists. He also received several smaller commissions for stained glass in the Freiburg area. The most serious of these was a commission for the church in Onnens, which the local authorities placed in 1902 in connection with the ongoing restoration of the Protestant church there. In the 13th-century church, disfigured in the 18th century, fragmentary Gothic paintings were uncovered, in the immediate vicinity of which Mehoffer's main stained glass window was placed. It complemented programmatically - with a motif of divine judgement - the surviving paintings of the wall enclosing the presbytery, depicting, among other things, hell and St Peter as guardian of the heavenly gates. This is one of the painter's most iconographically traditional religious works, perhaps due to the context of the place and the confession of the community imposed here: a symmetrical, archaic composition with a frontally depicted Christ seated on a throne and the archangels flanking his figure at the top, while in the lower part there are stylised representations of the mouth of hell and saved souls.

Stylistically, the stained glass is close to Mehoffer's designs for the Wawel Cathedral, created at the same time. The second smaller stained glass window is purely ornamental in nature: floral motifs in typical Art Nouveau styling. Both were realised in the excellent Freiburg atelier of Kirsch-Fleckner, with whom the artist constantly collaborated on work for the cathedral. As a result, despite their subdued colour scheme, the stained glass windows are characterised by a virtuoso nuancing of light effects.