By 1630 he had attained the rank of "Obristwachtmeister", and after distinguishing himself at the first Battle of Breitenfeld, where the Imperial army was destroyed and Mercy wounded, he commanded a regiment of foot with the rank of "Obrist" on the Rhine. He repelled a Swedish attack led by Gustaf Horn on Konstanz in 1633. For his brother Ludwig (born 1614), who died of his injuries at the age of 19 on 6 October 1633 shortly after the last attack by the Swedes, Franz von Mercy had an artistic bronze epitaph made in the Konstanz Minster, which is still preserved today. On 2 March 1634, Mercy was taken prisoner in a battle near Thann against the Rhine Count Otto Louis of Salm-Kyrburg-Mörchingen. He was exchanged and from April onward he defended Rheinfelden against a Swedish siege, surrendering on 29 August after running out of food.