This was an important advance in the development of the bishops' position as a secular ruler in his temporalities, forming a Hochstift of imperial immediacy since.

Bishop Otto von Rietberg had to contend with Cologne; in 1281, when only bishop-elect, he received the regalia from Rudolph of Habsburg, and full judicial power (except penal judicature).

Heinrich III Spiegel zum Desenberg (1361–80), also Abbot of Corvey, left his spiritual functions to a suffragan; in 1371 he rebuilt the Burg Neuhaus at Paderborn.

Wilhelm Heinrich van Berg, elected 1399, sought to remedy the evils which had crept in during the foregoing feuds, but when in 1414 he interested himself in the vacancy in the Archbishopric of Cologne, the cathedral chapter in his absence chose Dietrich III of Moers (1415–63).

The wars of Dietrich, also Archbishop of Cologne, brought heavy debts upon the bishopric; during the feuds of the bishop with the city of Soest (1444–49) Paderborn was devastated.

The countships of Lippe, Waldeck, and Pyrmont, the part of the diocese in the County of Ravensberg, and most of the parishes on the right bank of the Weser became Protestant.

Dietrich IV of Fürstenberg (1585–1618) restored the practice of the Catholic religion, built a gymnasium for the Jesuits, and founded the University of Paderborn in 1614.

While the bishopric as a state had been permanently dissolved, the Roman Catholic Diocese of Paderborn was recreated by Pope Pius VII in 1821.