Commissioned a major in the First American Regiment on October 22, 1790, the next year Ziegler served as second-in-command under Major Jean François Hamtramck, and defending the baggage train for General Arthur St. Clair in another expedition into the Northwest Territory. St. Clair met with even more disastrous results than Harmar at St. Clair's Defeat. Ziegler performed well, covering the retreat of the fleeing Americans. Ziegler was placed in command of the western forces when St. Clair was recalled for a court of inquiry. Once again Ziegler was called to testify, and again he supported his commander. Disturbed by disputes and jealousy in the officer corps, he resigned from the army on March 5, 1792.