GM Neu commended him to Feldmarschall Albert Casimir, Duke of Teschen for his untiring efforts and exceptional skills on 1 December 1794.

He then joined the renewed effort to relieve the Mantua, serving on the staff of Feldzeugmeister József Alvinczi, helping to plan the campaign, which ended in a narrow defeat by Bonaparte at the Battle of Arcole.

[3] His own plan for the Battle of Rivoli provided for three widely separated striking forces and unrealistically called for one flanking column to march across mountainous terrain in January.

[6] 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.

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.

Nevertheless, Weyrother was appointed military adviser to the new Foreign Minister, Graf Ludwig von Cobenzl in the negotiations following the Armistice of Steyr, which led to the Peace of Lunéville in 1801.