After the Battle of Stångebro during the War against Sigismund in 1598, Princess Anna fled with Sigismund to Poland, while Margareta remained; her spouse having been given command of Kalmar by Sigismund. In May 1599, her spouse and her brother-in-law were executed as followers of Sigismund by Charles IX of Sweden during the Kalmar Bloodbath. Margareta fled to Sigismund and Anna in Poland, where she accused her brothers Erik Brahe (1552–1614) and Magnus Brahe (1564–1633) of complicity in the death verdict of her spouse. She was provided with a pension by Sigismund for her loyalty and settled with her children in Denmark. In 1628, she was given permission to return to Sweden, where she died ten years later. She was the paternal aunt of Margareta Brahe.