However, in 1239, the conflict between her father and husband erupted into open warfare, when Skule had himself proclaimed king in Nidaros.

According to the Haakon Saga (Codex Frisianus), Margaret burst into tears when she was informed of her father's rebellion, and mourned his death greatly.

Queen Margrete is not described very closely as a person, and does not appear to have participated in politics, though she apparently protected her economic rights.

Margrete was also, at an unknown date before 1245, the first witness to Haakon's official confirmation of the authority of the church and the crown over Stavanger.

In the autumn of 1264, she accompanied her son Magnus on a visit to Rissa Abbey in Trøndelag, which was founded by her father, and where she likely spent her last years from 1267.