400 years later another fire raged and destroyed large sections of the cathedral on December 11, 1598. This afforded Archbishop Wolf Dietrich the opportunity to tear down the damaged cathedral and to make plans for its reconstruction. The Salzburg residents were extremely outraged at the archbishop’s ruthless actions. Not only were valuable sculptures and gravestones of the archbishops destroyed but the cathedral cemetery plowed under and the bones of the dead dumped on the debris. His quarrel with Bavaria over salt mining rights led to his arrest and imprisonment in the Hohensalzburg Fortress by his nephew and successor, Markus Sittikus von Hohenems, which put a bitter end to the various construction projects Wolf Dietrich had planned.

After Wolf Dietrich’s death the architect Santino Solari was commissioned by Archbishop Markus Sittikus to rebuild the Cathedral, which became the first early Baroque church north of the Alps. Markus Sittikus did not live to see the festive consecration of the Cathedral by Archbishop Paris Lodron during the chaos of the Thirty Years’ War on September 25, 1628. Through Paris Lodron’s clever diplomacy, the heavily fortified city escaped most of the hardships of the Thirty Years’ War so that the consecration of the Cathedral became the largest and most pompous festival that Salzburg ever experienced. The centuries of sovereign rule by the Salzburg prince bishops was ended by the Napoleonic Wars. With the dethroning of the last prince bishop, Hieronymus von Colloredo, the first Habsburg, Ferdinand III, Grand Duke of Tuscany, brought Salzburg under his rule.