The scope, responsibility and structure of the Würzburg State Archives are characterised by a long and centuries-old tradition. An archive-like institution can be traced back to the early Middle Ages in the vicinity of the cathedral monastery. Soon, not only the cathedral chapter, whose archives always remained in the vicinity of the cathedral, but also the bishops of Würzburg maintained their own archives, thus ensuring archival continuity in Würzburg. While the bishops initially housed their archives in a corner tower in the Marienberg Fortress, they found a new home in the Residenz when the splendid city palace was built in the 18th century.

The archive experienced its greatest disruption during the Napoleonic era. After the end of the Prince-Bishopric of Würzburg and the transfer of Würzburg to Bavaria, the Würzburg archive was declared the central archive for the Bavarian administrative district of Lower Franconia. Countless documents from the dissolved rulers of the Old Empire were transferred to the archive, including: Charters, official records and files from the prince-bishop and cathedral chapter of Würzburg, the imperial city of Schweinfurt, dissolved monasteries, imperial knighthood archives, documents from Fulda Abbey (due to the offices of Brückenau and Hammelburg) and, last but not least, large parts of the Mainz state government archive, which had last been located in Aschaffenburg during the flight from the French.

Since 1921, under the name "Staatsarchiv Würzburg", the archive has been responsible for securing and preserving the written records of all authorities and courts located in the administrative district of Lower Franconia. Only once could this task not be fulfilled, when in the course of the devastating air raid on Würzburg by British bombers on the night of 16 March 1945, the archive rooms in the Residence were also hit and caught fire. Numerous valuable documents and files as well as the old finding aids were destroyed.

Today, the Würzburg State Archives contain around 27 kilometres of archive material, including around 65,000 documents and almost 150,000 official records and files. The approx. 1,400 plans in the map collection are particularly splendid. Since the 1970s, the Würzburg State Archives have also acted as the central centre for the records of the notary's offices in the Bamberg Higher Regional Court district (Upper and Lower Franconia); around 6.3 million notarial deeds have already been handed over to the archives.The Würzburg State Archives currently occupies over 60 rooms in the north wing of the Würzburg Residence as well as a modern repository in a wing of the core castle on Marienberg Fortress.

A decision by the Bavarian state government in 2015 determined that the two repositories of the State Archives should be merged into a single location in a new building in Kitzingen am Main. A modern and functional archive building is currently under construction there; the move from Würzburg to Kitzingen is planned for 2026.