In 1798, Wallis was commanding General of Venetia. The following year, during the War of the Second Coalition, he commanded part of the Habsburg army in Swabia under Archduke Charles. He led the third column in its assault on the French positions in the Habsburr victory over General of Division Jordan's Army of the Danube at the Battle of Ostrach on 21 March. A week later, and in the French defeat at Stockach on 25 March, he commanded the right wing. From 14 to 25 April, while Archduke Charles was indisposed, Wallis assumed command of the main Habsburg army quartered on the shore of the Rhine River. A few weeks later, he commanded the reserve in the First Battle of Zürich on 4 June, where General of Division André Masséna, now commanding the Army of the Danube and the Army of Switzerland, was defeated and forced to withdraw across the Limmat river. During the battle, Wallis led five battalions of grenadiers in storming the French positions on Mount Zürich. He was badly wounded, and died five weeks later, on 19 July 1799.