At the time of his birth, his father still carried the title Elector of Saxony, but he lost it in 1547 after his defeat and capture by the Emperor Charles V due to his support of the Protestant Reformation.

Johann Frederick was released and forced to adopt the lesser title of duke of Saxony in an area substantially smaller than his former lands in Thuringia.

Johann Wilhelm was a member of the House of Wettin, which had served as the protecting power of Protestantism in Germany since the time of Frederick the Wise, yet he allied himself with the Catholic King of France against the Protestants Huguenots.

Johann Wilhelm retained only the smaller part of the duchy, the region around Weimar, but he added the districts of Altenburg, Gotha, and Meiningen to his territories.

In Heidelberg on 15 June 1560 Johann Wilhelm married Dorothea Susanne of Simmern, daughter of Frederick III, Elector Palatine.