At the time, this marriage was politically sensitive, because her elder brother, Hereditary Prince Christian of Saxe-Altenburg, had already died young and her younger brother, Frederick William III, who had succeeded her father as Duke, was still under the guardianship of her uncles and did not have children yet.

Duke Frederick William III died of smallpox, only six months after Johanna Magdalena married.

She created prayer books, collections of proverbs and didactic writeups and gave these to relatives and members of the court.

She died on 22 January 1686, at the age of 30 and was buried in a resplendent pewter coffin in the church of Neu-Augustenburg castle.

She married on 25 October 1671 in Altenburg with John Adolph I, the son of Duke Augustus of Saxe-Weissenfels from his marriage to Anna Maria of Mecklenburg-Schwerin.