The unit was first sent to Key West, Florida, then to Pensacola, Florida. Soldiers from the 91st New York took part in the raid on Bagdad, Florida. Later they were part of a raid into southern Alabama. They captured the steamboat Bloomer from the Town of Geneva, in what was then Coffee County, in the latter part of 1862, and early 1863. Lt. James H. Stewart led the raid, and was accompanied by a naval unit commanded by Acting Master Elias Bruner of the USS Charlotte. Although no shots were fired, due to the raid, Alabama raised defensive Confederate troops in the area which were stationed in southern Alabama until needed elsewhere. The regiment participated in the occupation of Baton Rouge, Louisiana, from December 1862 to March 1863. Then they took part in operations in western Louisiana. From May 24, 1863, to July 9, 1863, the 91st New York took part in the Siege of Port Hudson, one of the last impediments to Federal control of the Mississippi. The regiment's next duty was at Fort Jackson, part of the defenses of New Orleans, as the garrison from July, 1863, to August, 1864. The regiment was then given veteran furlough until October, 1864. In October, 1864, the regiment was transferred to the defenses of Baltimore, Maryland, as part of the VIII Corps, previously the Middle Department to February, 1865. In February, 1865, the regiment was transferred to the 1st Brigade, 3rd Division, V Corps, Army of the Potomac to June, 1865. They took part in the Siege of Petersburg and the Appomattox Campaign, including the Battle of Lewis's Farm, Battle of White Oak Road, Battle of Five Forks, Third Battle of Petersburg and pursuit of General Robert E. Lee's Army of Northern Virginia to Appomattox Court House, Virginia, where Lee surrendered his army on April 9, 1865. As part of a post-war reorganization, they briefly became the 3rd Brigade, 3rd Division, V Corps for duty at Washington, D.C. until July 3, 1865, when they were mustered out. The regiment lost 3 officers and 110 enlisted men killed and mortally wounded and 1 officer and 184 enlisted men by disease for a total of 298 men, during their service.
Commanders
Colonel Jacob van Zandt - court-martialled and dismissed, February 1865