During Anna's rule, the armed conflict with the Lordships of Esens, Stedesdorf and Wittmund flared up one more time, when Count John II "the Mad" of Harlingerland seized a strip of land at the Accumer Deep.

In 1558, she abolished the law that the first born would succeed as sole ruler of the county; instead, power was to be shared between her three sons, Edzard, Christopher and Johan.

This was meant to prevent Swedish dominance in view of the wedding between her son Edzard to princess Katharina Vasa of Sweden (1559).

It also implied a continuation of the religious balance, with Johan being a Calvinist and Edzard being Lutheran and neither of them able to establish their faith as the only religion allowed in the county.

Menso Alting had only been preacher at Emden for a short time, when Countess Anna died there on 24 September 1575.

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