From the sixteenth to the eighteenth centuries, it was often held in personal union with one or more of the nearby ecclesiastical principalities of Cologne, Paderborn, Osnabrück, Hildesheim, and Liège.

Münster was bordered by the United Provinces to the west, by Cleves, Vest Recklinghausen, and Mark in the south, Paderborn and Osnabrück in the east.

The diocese also included districts remote from the bulk of its territory, namely, the five Frisian hundreds on the lower Ems (Hugmerki, Hunusgau, Fivelgau, Federitgau, and Emsgau).

Most of the territory over which the bishop eventually exercised sovereign rights lay north of the River Lippe, extending as far as the upper Ems and the Teutoburg Forest.

With the overthrow of Henry the Lion, Duke of Saxony, the last obstacle in the way of the complete sovereignty of the bishops was removed, and Hermann appears as a great feudatory of the empire.

During the episcopate of his second successor, Dietrich III of Isenberg-Altena (1218–26), the position of the bishop as a prince of the empire was formally acknowledged in 1220 by Frederick II.

In 1457, after his death, a compact was made by which Eric of Hoya received a life income, and the privileges of the city were confirmed, while both parties recognized the new bishop appointed by the pope, John II, Count Palatine of Simmern (1457–66).

Scarcely any opposition to the innovation was made by the next bishop, Franz von Waldeck (1532–53), who from the first planned to aid the Reformation in his three prince-bishoprics of Münster, Minden, and Osnabrück, in order to form out of these three a secular principality for himself.

He was obliged, indeed, for the sake of his endangered authority, to proceed against the Anabaptists in the city of Münster; but he did little for the restoration of the Faith, and at last joined the Smalkaldic League.

William of Ketteler (1553–57) was more Protestant than Catholic: although he regarded himself as an administrator of the old Church, and took the Tridentine oath, he refused to comply with the demands of Rome, and resigned in 1557.

The western part of the Frisian district under the ecclesiastical jurisdiction of Münster was transferred, in 1569, to the newly founded bishoprics of Groningen and Deventer, and with them fell into Protestantism.

Christoph Bernhard von Galen (1650–78) was equally efficient both as bishop and as secular ruler; he forced the refractory city of Münster, after a long siege, to acknowledge his sovereign rights, succeeded in freeing his territory from foreign troops, gained parts of the Prince-Archbishopric of Bremen and of the Prince-Bishopric of Verden in a war with Sweden (taking part in the Bremen-Verden Campaign), restored church discipline, and established a school system for his territory.

However, at the election of an auxiliary bishop, von Fürstenberg was defeated by Maximilian Franz of Austria, who later succeeded to both the sees of Münster and Cologne (1784–1801).

Maximilian Franz fled Bonn in 1794 at the arrival of French revolutionary troops, who were to remain in permanent occupation of the part of the bishopric located on the left bank of the Rhine.