Since at the time Johann's older brother Frederick William I was also under age, the duchy of Saxe-Weimar (originally awarded to Johann) was governed by a regency.

In 1586 Frederick William reached adulthood and took full control of the duchy, including Weimar.

However, he died in 1602 and the full duchy was inherited by Johann, because Frederick William's sons were underage.

Johann was more interested in natural sciences and art than politics, and therefore only against his will took over the regency of the duchy on behalf of his nephews.

Finally, Johann and his nephews made a treaty dividing the duchy: Altenburg was taken by the sons of Frederick William I, and Weimar-Jena was retained by Johann.