He was the second eldest son of John I of Werle and Sophie of Lindow-Ruppin.
After Nicholas's death in 1316 it was decided to divide the territory, and John took control over part of the territory called Werle-Güstrow, and Nicholas's son John III, took control over the part called Werle-Goldberg.
However, the Dukes of Pomerania took Rugen, leading to the Rügen War of Succession.
John II reduced his debts by prosecuting Jews for host desecration.
In 1311, John II married Mechtild (born: c. 1295; died: between 24 October 1333 and 14 March 1344), a daughter of Duke Henry I of Brunswick-Grubenhagen.