Salzburg entered a cultural renaissance in the 16th Century, but its political significance began to wane. The last prince-archbishop who attempted to amass more territories was Wolf Dietrich von Raitenau, who declared an unsuccessful war on Berchtesgaden in 1611. Despite this, von Raitenau is noted for commissioning the Mirabell Palace and reconstructing the centre of Salzburg.

Raitenau was succeeded by archbishop Markus Sitticus von Hohenems, who erected the Hellbrunn Palace and the new Salzburg Cathedral. Due to diplomatic talents of one man, Count Paris von Lodron, Salzburg remained intact throughout the Thirty Years War. Moreover, the University of Salzburg opened in 1622. A large number of notable buildings in Salzburg date from the late 17th and early 18th Centuries, which include the Collegiate Church, St John’s hospital, the Presbytery, the Ursulinen Church and Church of the Holy Trinity, which were all commissioned by Archbishop Johann Ernst Count Thun.

On October 31, 1731, Archbishop Count Leopold Anton von Firmian signed an edict of expulsion against Protestants living in the territory of the province, ordering them to change their beliefs, or be banished. This date marked the 214th anniversary of Martin Luther's nailing of his Disputation on the Power and Efficacy of Indulgences (95 Theses) in Wittenberg, challenging, among other issues, the authority of the pope, the nature of penance and the usefulness of indulgences. His theses sparked a debate that eventually led to the 16th Century Protestant Reformation.

The archbishop’s belief was that his edict would drive away many infidels, but it had quite the opposite effect, with some 22,000 people publicly professing Protestantism. Von Firmian reacted by giving the converts three months to sell their lands and leave. He personally confiscated much of the land for use of his own family and ordered the burning of all Protestant bibles and books. Young children were also taken away from their parents, in order to be raised by Catholics. Those who did not own land had to leave in eight days. They crossed the mountains in the worst of winter. The story of these exiles forms the basis of Goethe's poem Hermann and Dorothea. Some aid was offered for these refugees, as they passed through various towns, but they could not find a place to call home. In 1732, King Frederick William I of Prussia, a Lutheran, accepted 12,000 of these migrants, who settled in East Prussia, a region on the southeast Baltic seacoast. Other groups settled in the present-day territories of Romania, Slovakia, Hanover, Berlin, the Netherlands and Debrecen.