His ability to recruit German-speaking immigrants to the Union armies received the approval of President Abraham Lincoln, but he was strongly disliked by General-in-Chief Henry Halleck.

Wounded in a skirmish, Sigel had to resign his command but continued to support the revolutionary war effort as adjutant general to his successor Ludwik Mieroslawski.

He then moved to Carthage, to cut off the retreat of pro-Confederate Missouri State Guard troops previously defeated by Lyon at Boonville.

In the subsequent Battle of Carthage on 5 July, Sigel's outnumbered force was driven back by the State Guard.

In the Battle of Wilson's Creek, on 10 August, he led a flanking column which attacked the rear of the rebel force, but was routed.

The army moved through Springfield into Arkansas, and met Confederate troops under Maj. Gen. Earl Van Dorn in the Battle of Pea Ridge on 8-9 March.

He commanded the I Corps in Maj. Gen. John Pope's Army of Virginia at the Second Battle of Bull Run, another Union defeat, where he was wounded in the hand.

Over the winter of 1862–63, Sigel commanded the XI Corps, consisting primarily of German immigrant soldiers, in the Army of the Potomac.

He had developed a reputation as an inept general, but his ability to recruit and motivate German immigrants kept him employed in a politically sensitive position.

Many of these soldiers could speak little English beyond "I'm going to fight mit Sigel",[5] which was their proud slogan and which became one of the favorite songs of the war.

They were quite disgruntled when Sigel left the XI Corps in February 1863, and was replaced by Major-General Oliver O. Howard, who had no immigrant affinities.

General-in-chief Henry W. Halleck detested Sigel, and managed to keep him relegated to light duty in eastern Pennsylvania until March 1864.

President Lincoln, for political reasons, directed Secretary of War Edwin M. Stanton to place Sigel in command of the new Department of West Virginia.

He was soundly defeated by Maj. Gen. John C. Breckinridge at the Battle of New Market, on May 15, 1864, which was particularly embarrassing due to the prominent role played by young cadets from the Virginia Military Institute.

In 1869, he ran on the Republican ticket for Secretary of State of New York, losing to the incumbent Democrat Homer Augustus Nelson.