Elisabeth and her children fled to Eisenach and then to her sister Dorothea Susanne of Simmern, who was married to her husband's brother, John William, Duke of Saxe-Weimar.

At the end of 1568, she moved back to Eisenahch, initially to the Zollhof court, then to the Wartburg and finally into the castle at Eisenberg In the following years, Elisabeth wrote a number of petitions to, among others, Emperor Maximilian II, Empress Maria and Anne, Electress of Saxony, trying to obtain the release of her husband.

In June and July 1578, Elisabeth traveled via Prague, where they unsuccessfully tried to meet Dowager Empress Maria, to Coburg where she met with her younger sister Dorothea Susanna.

In 1583, Elisabeth traveled in the period from March to August, via Prague and Coburg to Weimar to attend on 5 May at the wedding of Frederick William I, Duke of Saxe-Weimar, with Sophie of Württemberg, and to meet Elector Augustus.

On her return journey, she visited her brother Louis VI, Elector Palatine, in Heidelberg, where she was accompanied by her sons.