During the Protestant Reformation of the 16th century, Osnabrück did neither completely stay Catholic nor completely switch to Protestantism. Instead, each parish decided on its own which elements of Protestantism it took over. This unique situation ended with the Peace of Westphalia of 1648, when parishes were divided up between the two religions. From then on, the bishops alternated between Lutherans and Catholic office holders; the Protestant bishops were appointed by the nearby Duchy of Brunswick-Lüneburg, and were generally cadet members of the ducal family.
The last Prince-Bishop of Osnabrück, the Lutheran Prince Frederick of Great Britain (1764–1803), later Duke of York, was, until his majority (1783), under the guardianship of his father, George III, king of the United Kingdom and Hanover. Frederick was notoriously made Bishop when 197 days old.
In the German Mediatisation of 1803, the Bishopric was dissolved and given to the Hanover branch of Brunswick-Lüneburg; the see, the chapter, the convents and the Catholic charitable institutions were finally secularized. The territory of the see passed to Prussia in 1806, to the Kingdom of Westphalia in 1807, to Napoleonic France in 1810, and again to Hanover in 1814. Klemens von Gruben, titular Bishop of Paros, was made vicar Apostolic, and as such cared for the spiritual interests of the Catholic population.