He was the only son of Rudolph, Prince of Anhalt-Zerbst, by his second wife Magdalene, daughter of John VII, Count of Oldenburg.

John succeeded his father in Anhalt-Zerbst at only four months of age; during his long minority, his paternal uncle Augustus of Anhalt-Plötzkau acted as regent in the principality.

Immediately after he reached adulthood and formally assumed the government of his state, John made Lutheranism the official religion of Zerbst.

In 1642 his uncle Louis of Anhalt-Köthen, admitted John to the Fruitbearing Society together with the Hofrat Konrad Balthasar Pichtel and the Hofjunker Joachim von Boeselager.

The late Count had made approximately this kind of stipulations in his testament – which said that the nephew John will inherit Jever, a Frisian lordship.