They removed the city council, which Edzard II had appointed from office and occupied the count's castle.
At the same time, the integration of the Calvinist refugees marked East Frisian society economically and religiously.
After the 1609 truce between Spain and the rebellious Netherlands, the port blockades were lifted and many refugees returned home.
At the same time, tensions arose between the East Frisian town of Emden and Count Edzard II.
This led to a religious division in the county, as John, like his mother and the majority of the citizens of Emden, was a Calvinist whereas Edzard was Lutheran.
Menso Alting, the reformed vicar in the Great Church in Emden, became a leading opponent of the power ambitions of count Edzard II.
Then Gerhard Bolardus, a member of the college of forty, held an impassioned speech, in which he called for the overthrow of the Count.
Alarmed by the news from Emden, Edzard II sent his secretary into the city to test the waters.
The college of forty elected by the citizens grabbed power and appointed four new mayors and eight councillors.
He offered the States-General to join the Netherlands as its eighth province in return for military support.
He stationed troops at the Knock peninsula, west of Emden, and ordered them to shoot at passing ships.
As the battle had clearly demonstrated the power relations in East Frisia, Enno III went into hiding until February 1603.
The city of Emden then sent representatives to the States-General to conduct negotiations, which led to the Agreement of the Hague of 8 April 1603.
The city and the Reformed southwestern part of East Frisia built close ties with the Calvinist church in the Netherlands.
Tolerance in matters of faith had disappeared and the Treaty of Greetsiel stipulated that only the Reformed religion could be taught in Emden.