The name Lindau was first mentioned by a monk from St. Gallen in a document of 882, stating that Adalbert, count of Raetia, had founded a nunnery on the island. However remains of an early Roman settlement dating back to the 1st century have been found in the district of Aeschach.
In 1180 the St. Stephan's church was founded. In 1224 the Franciscans founded a monastery on the island. In 1274/75 Lindau became an Imperial Free City under King Rudolph I. In 1430, about 15 of the town's Jews were burned at the stake after being accused of murdering a Christian child. In 1528, Lindau accepted the Protestant Reformation. The city first followed the Tetrapolitan Confession, and then the Augsburg Confession. After the Thirty Years' War, in 1655 the first Lindauer Kinderfest (children's festival) was held in memory of the war time.