One of a group of three, known as "Thugut's Benjamins" (trusted assistants to the Foreign Minister Johann Amadeus Francis de Paula, Baron of Thugut, during the campaign of 1799, Weyrother served as chief of staff to Feldzeugmeister Pál Kray, where he distinguished himself at Legnago (26 March), Magnano (5 April) and, now serving as liaison officer with the Russian Field Marshal Alexander Suvorov, at Novi on 15 August. He then planned the epic march of the Russian troops under Alexander Suvorov across the Saint Gotthard Pass. Promoted to "Oberst" (colonel) on 5 February 1800, Weyrother was given command of Infanterie-regiment Nr. 7 "Schröder", which was part of the army in Germany under Pál Kray, but a further wound and the strains of campaigning led to his leaving the army to recuperate. Recalled in the autumn of 1800, Emperor Francis II assigned him to be chief-of-staff to the 18-year-old Archduke John of Austria, the new commander of the army in Bavaria, and his "Adlatus" (chief adviser) Franz von Lauer. Believing Jean Moreau's French army to be in retreat, Weyrother organised an aggressive pursuit through heavily forested terrain by four non-mutually-supporting columns. Instead, Moreau stood his ground, sprang an ambush, and enveloped the Austrian left flank. The resulting Battle of Hohenlinden turned out to be a catastrophe for the Austrians, effectively ending the War of the Second Coalition. Nevertheless, Weyrother was appointed military adviser to the new Foreign Minister, Graf Ludwig Cobenzl in the negotiations following the Armistice of Steyr, which led to the Peace of Luneville in 1801.