In 1564 Ferdinand II, Archduke of Austria received the rulership over Tirol and other Further Austrian possessions administrated from Innsbruck up to the 18th century. He had Schloss Ambras built and arranged there his unique Renaissance collections nowadays mainly part of Vienna's Kunsthistorisches Museum. Up to 1665 a stirps of the Habsburgian dynasty ruled in Innsbruck with an independent court. In the 1620s the first opera house north of the Alps was erected in Innsbruck (Dogana).

In 1669 the university was founded. Also as a compensation for the court as emperor Leopold I again reigned from Vienna and the Tyrolean stirps of the Habsburg dynasty had ended in 1665.

During the Napoleonic wars Tyrol was ceded to Bavaria, ally of France. Andreas Hofer led a Tyrolean peasant army to victory on the Berg Isel against the combined Bavarian and French forces, and then made Innsbruck the centre of his administration. The combined army later overran the Tyrolean militia army and until 1814 Innsbruck was part of Bavaria. After the Vienna Congress Austrian rule was restored. The Tyrolean hero Andreas Hofer was executed in Mantua; his remains were returned to Innsbruck in 1823 and interred in the Franciscan church.
Main article: Bombing of Innsbruck in World War II

In 1938 Austria was annexed by Nazi Germany in the Anschluss. Between 1943 and April 1945, Innsbruck experienced twenty-one bomb attacks and suffered heavy damage. The KZ Innsbruck-Reichenau concentration camp was located here.[1]

In 1929, the first official Austrian Chess Championship was held in Innsbruck. The winners were Erich Eliskases and Eduard Glass.