[1] After the death of her mother in 1551, she as well as her siblings were placed in the care of Christina Gyllenstierna and then under her aunts Brita and Martha Leijonhufvud before her father's remarriage to Catherine Stenbock.

The marriage took place in a double wedding when her half brother King Eric XIV married Karin Månsdotter on 4 July 1568.

Sophia did not want the marriage—she refused and stalled preparations for the wedding, which prevented it from taking place in June 1567 as first planned when Eric married Karin for the first time.

During the deposition of Eric XIV, Sophia, Magnus evacuated Elizabeth and Catherine Stenbock by boat, and took them to the rebellious John in Uppsala.

According to the chronicle of Aegidius Girs, Sophia became insane by the treatment she was given by Magnus, who: "...showed his princess all unkindness, spit and shameful slander, that she of the sorrow was caused great weakness of the head.

He also came in conflict with John III in 1576 when he forbid his subjects in Sophia's fief from paying taxes and executing their working duty for the crown.

In 1577, reports said that Magnus prevented Sophia from receiving letters from her family and accepting invitations, and isolated her from the outside world.

John had the Emperor ban Magnus from making slanders against Sophia that could blacken her name and endanger her son's inheritance and her right to her dower lands.

[2] She is not described as an efficient administrator of her estate and court: she was often forced to ask for economical assistance because of her misused lands, and her court was unstable with frequent changes of staff: she changed her chamberlain twenty-one times and her housekeeper twenty-three times during these years.