During the Protestant Reformation, Count Hoyer VI of Mansfeld-Vorderort (1477–1540) remained loyal to his Catholic faith, but the family's Mittelort and Hinterort branches sided with Martin Luther.

Count Albert VII of Mansfeld-Hinterort (1480–1560) signed the Protestant Augsburg Confession in 1530 and joined the Schmalkaldic League, a defensive confederation of Protestant princes which ultimately lost the Schmalkaldic War over Saxony to the forces of Emperor Charles V but gained Lutheranism's recognition as an official religion within the Holy Roman Empire, letting princes determine the official religion within their lands.

The Hinterort branches died out in 1666, but the Mansfeld-Vorderort line lasted until 1780, when it too became extinct and Eisleben came directly under the Electorate of Saxony.

After the Napoleonic Wars ended, the Vienna Congress assigned Eisleben to the Kingdom of Prussia, which had long been allied with House of Welf which held the Duchy of Magdeburg, and after secularization in 1680 was administered by the Elector of Brandenburg.

In 1947, after World War II, Eisleben became part of the new state of Saxony-Anhalt within the German Democratic Republic (GDR).

Between 2004 and 2010, the town Eisleben absorbed 10 former municipalities: Volkstedt in 2004,[3] Rothenschirmbach and Wolferode in 2005,[4] Polleben and Unterrißdorf in 2006,[5] Bischofrode, Osterhausen and Schmalzerode in 2009,[6] and Burgsdorf and Hedersleben in 2010.

It closed in 1524, during the religious wars sometimes associated with Martin Luther, but reopened on a smaller scale until 1542, after which it became secularized, and controlled by local farmers.

Cistercian nuns from Seligenthal in Bavaria moved into the cloister starting circa 1999,[11] Since 2006 Helfta has been on the southern portion of a major European cultural route, the Romanesque Road.

Danish poet Hans Christian Andersen came to Eisleben while researching Lutheran links as well as touring through Saxony and the Harz Mountains in 1831.