He probably spent his early years in the Weinfelden Castle, before his father sold it to the Fugger family in 1555.

His nephew, Johann Konrad von Gemmingen, was subsequently elected as Bishop of Eichstätt.

Pope Gregory XIV confirmed his appointment on 10 May 1591, and he was consecrated as a bishop on 25 August 1591.

As bishop, Johann Otto promoted Roman Catholicism and introduced many reforms.

Johann Otto von Gemmingen died in Dillingen an der Donau on 6 October 1598.