He continued the harsh measures of the Counter-Reformation initiated by his predecessors, invited Franciscan and Augustinian friars, and in 1589 had all Protestants expelled from the city of Salzburg.

In his later years, however, he developed a milder attitude and initiated reforms of the liturgy and the administration of the episcopal lands, which alienated the Roman Curia.

Perceptive, well-read, and a follower of Niccolò Machiavelli's ideas, Raitenau considered himself a genuine Renaissance prince of an absolutist state.

He won fame not only as an art collector but also as a builder who significantly promoted the spread of the Baroque architecture north of the Alps: When Salzburg Cathedral was devastated by a fire on the night of 11 December 1598, he had plans set up for a lavish reconstruction by the Venetian architect Vincenzo Scamozzi, who also drew up a master plan for the adjacent Residenzplatz square and designed the Salzburg Residenz.

Deserted by his cathedral chapter and abandoned by Emperor Rudolf II, Raitenau on his flight to Carinthia was captured, deposed and imprisoned for life by his nephew and successor, Mark Sittich von Hohenems, first at Hohenwerfen Castle and later in Hohensalzburg.