During his reign, Edzard came into conflict with the city of Emden. Edzard was a staunch Lutheran while the city of Emden was mostly Calvinistic. In 1595 Emden revolted and, after an intercession by the Calvinistic Dutch Republic, Edzard was forced to accept a large degree of independence from Emden.
Edzard II had a dispute with his dominant mother, Anna. She had abolished his right of primogeniture, in an attempt to curb the influence of the Swedish royal family. She decreed that Edzard should rule East Frisia jointly with his younger brothers Johan and Christopher. When Christopher died early, Edzard ran into a strong and almost hateful rivalry with his brother Johan II. The power struggle between two increasingly hamstrung their government. After Johan died in 1591, Edzard became the sole ruler, but his authority had been severely hit by the ongoing conflict.
At the request of the Estates, Edzard founded the High Court in Aurich in 1593.
In 1595, the city of Emden revolted. In the course of this Emden Revolution, the Cirksena family were driven out of Emden. Under pressure from the Dutch States General, Edzard signed on 5 July 1595 the Treaty of Delfzijl, which gave Emden a large degree of independence.
During Edzard's reign, the Counts of East Frisia definitively lost the Lordship of Jever. Maria of Jever, the last baroness, died and left her territory to the Counts of Oldenburg.
Edzard died on 1 March 1599. The Great Church at Emden refused to allow him to be buried in the Cirksena family vault, because he was a Lutheran and it was a Reformed church. He was buried on 13 May 1599 in the St. Lambert ChurchinAurich. He was the first member of the Cirksena family to be buried there. However, all later family members were buried in this church, until the family died out in 1744.
