[1][better source needed] Six years after her marriage, her father inherited the Duchy of Saxe-Altenburg and assumed new arms and titles.

On 5 December 1666, Elisabeth Dorothea married Louis VI, Landgrave of Hesse-Darmstadt at Schloss Friedenstein at Gotha.

She bore her husband eight further children, two daughters and six sons; one died in infancy and another was killed in battle ten months before her own death.

The Imperial Court (Reichskammergericht) demanded that she reign jointly with a group of councillors led by Weiprecht von Gemmingen, but the politically wise and energetic Elisabeth prevented them from taking their oaths; this relegated them to the position of advisors and allowed her free rein.

On the death of William Christoph, Landgrave of Hesse-Homburg in 1681, Elisabeth Dorothea successfully challenged the Homburg branch of the family over ownership of Bingenheim Castle, claiming that the area rightfully belonged to the Darmstadt branch because it had been given to Princess Sophia Eleonore of Hesse-Darmstadt as a dowry when she married William Christoph, Landgrave of Hesse-Homburg.