Eitel Friedrich was loyal to the Catholic Church and therefore supported the Habsburg during the Thirty Years' War.

In the war, the fortress developed into a focal point and was besieged and devastated by the Swedes and Württembergers in 1634.

The castle was recaptured by Imperial troops the next year, and remained under Habsburg control until 1798 against a payment of 5,000 guilders annually.

The Thirty Years' War had impoverished the people in Hohenzollern-Hechingen and Eitel Friedrich was also faced with serious financial problems, forcing him to sell several attractive fiefs.

In 1653, Eitel Friedrich became a Prince of the Holy Roman Empire and was admitted to the Imperial Diet in Regensburg.