Between 500 and 788, Regensburg was the main residence of the Bavarian dukes, the Agilolfingians. During this period, it became diocese and therefore still is one of the oldest cathedral towns in Germany although it turned Protestant in 1542.
In the 6th century, Regensburg was made the first capital of Bavaria.
A period of wealth started in the 12th century when trade with cities throughout Europe flourished. This also boosted construction works and architecture. Many Romanesque and Gothic buidlings were constructed that still are a major part of the historic city. The Stone Bridge that was built between 1135 and 1146 represented the wealth of the city and also was a miracle of medieval engineering. During this period as well, Konrad III. and Emperor Frederick I. Barbarossa entered upon two of the crusades. Also under the reign of Frederick I. Barbarossa, the Wittelsbachs established as ruling dynasty.
In the 13th century, Regensburg became a free imperial city with the right to set up a mayor and a council. The conflict with the bishop of Regensburg and the dukedom Bavaria started.
After a long struggle between the church and the council, Regensburg became Protestant in 1542 which did not solve the problem.
From the end of the 16th century onwards, the Imperial Diets were held only in the Imperial Hall of the City Hall of Regensburg. Since 1663, these Diets were not dismissed any more until the beginning of the 19th century and are therefore called "Perpetual Imperial Diet". In 1748, Prince Alexander Ferdinand von Thurn und Taxis was appointed to be principal commissioner (i.e. the Emperor's representative at the Imperial Diet).
The last meeting of the Perpetual Imperial Diet took place in 1803 when the Holy Roman Empire was dissolved. After having been attacked and taken by Napoleon's troops, Napoleon forced the bishop Dalbert to hand over Regensburg to the Kingdom of Bavaria which was major setback with regard to the independence of the city although Regensburg was quite poor at that time.
In 1838, Regensburg became the capital of "Upper Palatinate and Regensburg" .
During the Second World War, the established Jewish community at the Neupfarrplatz was terrorized and expelled. Although Regensburg was seriously attacked by air raids, the historic city center was hardly destroyed.
In 1945, Regensburg already had more than 100,000 citizens.
In 1965, the building works of the University of Regensburg started, in 1992 the University hospital was opened. In addition, many large companies, for example Siemens, BMW, Infineon, Toshiba are located here now.