In 1558 the primogeniture of John's mother, the Countess Anna was abolished, presumably to stem the impact of the house Vasa in the county, which was based on the marriage of her eldest son Edzard with Catherine Vasa of Sweden, the eldest daughter of King Gustav I of Sweden.

This led to a de facto division of East Frisia, because Johan, like his mother, was a Calvinist, whereas Edzard II was a Lutheran.

After the death of their brother Christoffel in 1566, the power struggle between Johan and Edzard worsened.

Johan blocked Edzard's exercise of sovereign power and strengthened the nobility and the citizens of Emden.

After Johan died in 1591, Edzard finally became the sole ruler of the County of East Frisia, but his authority had been severely hit by the ongoing conflict.