On 1 February 1549, just thirteen years of age, he was officially admitted to the University of Wittenberg, where, among others, he studied with the theologian Georg Helt.

The death of his uncle George III without male heirs permitted him and his brothers, Karl I and Bernhard VII, to inherit Anhalt-Plötzkau in 1553, while the death of his uncle Joachim I permitted him and his surviving brother Bernhard VII to inherit Anhalt-Dessau in 1561.

In 1570 the death of his last surviving brother, Bernhard VII, left him as sole ruler of all the Anhalt states, which were finally unified for the first time since their first partition in 1252.

Joachim Ernest was a typical Renaissance monarch who generously supported the arts and culture.

Also, he ordered the son of his chancellor, Tobias Hübner, to create a description of the famous knight's games (German: Ritterspiele) that took place at the Dessau court.