During the formation of the Polish Armed Forces in late October 1918, Zagórski was appointed Vice-Chief of the Polish Army's General Staff. However, on November 10 - only three weeks later - he was forced to resign. He was recalled to the Army at the start of Polish-Soviet border conflicts which soon erupted into the Polish-Bolshevik War. During the war, he was Chief of Staff of the Polish Northern Front, which was then led by General Józef Haller. He participated in the Battle of Warsaw.