Johann was the son of John Albert I, Duke of Mecklenburg-Güstrow and Schwerin (1525–1576), and his wife Duchess Anna Sophia of Prussia (1527–1591).

He immediately faced problems he was ill-equipped to deal with, including massive debt and his uncle Christopher's demands for territorial concessions.

Since suicides could not be buried in hallowed ground, a story was concocted which alleged that Johann had been killed by the devil as part of a pact with two women from Schwerin.

The women were questioned: Katharina Wankelmuth, who died from the effects of torture, and Magdalena Rukitz, who was burned at the stake.

On 17 February 1588 Johann married Sophia (1 June 1569 – 14 November 1634), a daughter of Adolf, Duke of Holstein-Gottorp, and his wife Christine of Hesse.