While the prince-bishopric's territory was comparatively small, it was very fragmented and its lands were dispersed over a wide area, from central Bavaria and Tyrol in the west to Austria, Styria and Carniola in the east (see map).

In 783, Bishop Atto von Kienberger acquired the town of Innichen (San Candido) in the South Tyrol after having delivered on his promise to the lord of the area, Duke Tassilo III of Bavaria, to build a Benedictine convent there.

In contrast to the prince-bishopric which was made of several disparate small enclaves, the diocese of Freising, administered by the same bishop, was very large and covered most of the surrounding duchy of Bavaria, including the capital Munich.

Like other parts of the Holy Roman Empire, Freising did not escape the ravages of the Thirty Years' War and while it paid the ransom demanded by the Swedish King Gustavus Adolphus in 1632, the city was still pillaged.

Freising was to reach its peak under Prince-Bishop Johann Franz Ecker von Kapfing und Liechtenech (1696–1727) who founded the first Hochschule (high school) in 1697 and carried out extensive renovations of the cathedral church on the occasion of the 1000th anniversary of the diocese (1724).

Like his predecessors, Bishop Abraham had been actively involved in missionary work among the Slavic populations east of the Alps, which explains why an area of Slovenia (Skofja Loka) was to become part of the distant Prince-Bishopric of Freising for several centuries.