After Gustavus Adolphus of Sweden conquered the area in 1631 during the Thirty Years' War, the castle was reconstructed as a Baroque residence.

After it ceased to serve as residence of the Bishops of Würzburg, the fortress saw repeated action in the wars of the late 18th and 19th centuries.

The fortress is located on a prominent spur of the 266-metre-high (873 ft) Marienberg, which rises about 100 metres over the Main river on the opposite side of the city of Würzburg.

After missionary work in the area led by Saint Kilian in the late 7th century, in the early 8th century, the Franks under Duke Hedan II constructed a chapel dedicated to the Virgin Mary and a fortification (earth ramparts and half-timbered houses) on the hill.

This was probably the first Christian church built of stone north of the Alps outside of the territory formerly controlled by Rome (i.e. east of the Rhine and on the far side of the Limes).

[1]: 2, 4–6, 20 [2]: 21 Saint Boniface came to Franconia in 719, by which time there was no longer a duke at Würzburg, and some of the local clergy practiced pagan customs.

Relations between bishop and town were fraught and the main reason for keeping an armed contingent stationed in the fortress.

After 1308, the palas was enlarged under Bishop Andreas von Gundelfingen [de] with construction paid for by the townspeople to compensate their liege lord for a riot that year.

When their political leader, Florian Geyer, went to Rothenburg ob der Tauber in early June to procure the heavy guns needed to attempt to breach the walls, the leaderless peasant army camped around the castle was outflanked by the professional army of the Swabian League.

[4] Also that year, sculptor Tilman Riemenschneider was imprisoned in the fortress and tortured along with the other members of Würzburg's city council, as punishment for allying themselves with the peasants.

[1]: 2, 12, 18 In 1631, after some days of fighting the fortress was taken by Swedish forces under Gustav II Adolf of Sweden in the Thirty Years' War.

In 1712, Charles VI was received by the Prince-Bishop at the castle, the last time a Holy Roman Emperor visited the fortress.

Shortly thereafter, in 1719/20 the court of the Bishops moved into a palace on the other side of the Main river which was later replaced by today's Würzburg Residence.

From 1805 to 1814, Marienberg was a fortress of the Grand Duchy of Würzburg, part of the Confederation of the Rhine, the puppet state of the First French Empire.

After the war, the Fürstenbau served as a barracks for the Landespolizei (state police), as a military depot and as an emergency accommodation (100 apartments).

[1]: 3, 26 [3]: 34 Towards the end of World War II, the Echterbastei served as a medical depot and then as a depository of cultural treasures.

[1]: 3 [3]: 34 [5] Given the repeated destruction of the fortress' structures over the centuries, most recently and significantly in the bombing of 1945, many of the edifices visible today have been reconstructed to a lesser or greater extent.

The inner court features the free-standing Romanesque 13th century Bergfried (keep), the Renaissance well house from 1603 and the Marienkirche (or St Mary's Church).

The Bergfried was originally known as Mittlerer Turm or Wartturm; the actual keep of the fortress was the predecessor of today's Kilianstum.

While the basic form of two cylinders placed on top of each other remains, the building's proportions were changed in the 13th century and the size of the windows increased.

[1]: 26–29 The Fürstenbau is surrounded by medieval fortifications (walls and towers), enclosing an outer ward known as Scherenbergzwinger (actually built under Bishop Otto von Wolfskeel).

[1]: 10, 14–17, 22–23 Beyond a moat, crossed by a stone bridge which in 1716 replaced the previous drawbridge, lie the outer ring of fortifications and the Echtersche Vorburg.

This three-wing part of the fortress includes a large horse trough in the middle of a courtyard, stables and the Echterbastei with Echtertor.

[3]: 10, 11 To the south is the squat Maschikuliturm, designed by Balthasar Neumann, architect of the Residenz, the last tower to be added to the fortress in the 1720s.

Since 1946, the Baroque Zeughaus (armory), originally built 1702-1712 but reconstructed after being destroyed in 1866 and 1945, houses the Museum für Franken, formerly the Mainfränkisches Museum [de], a collection of Franconian works of art from the Middle Ages to the Baroque period, including world-famous Gothic sculptures by Tilman Riemenschneider.

Founded in 1913 as Fränkisches Luitpoldmuseum in the town, the museum's previous location was destroyed by British bombers in March 1945.