Joseph Abbot was commissioned as a 1st Lieutenant with the 7th New Jersey Volunteers on September 18, 1861 for Company E. He served through the Battles of Williamsburg and the Peninsular Campaign as an aide-de-camp to General Joseph Hooker.

He advanced to Captain and commander of Company E on May 27, 1862, and led Company E through the the Seven Days Battles and the 2nd Bull Run Campaign. He was shot in the forehead and killed instantly during the 2nd Battle of Bull Run. Documentation suggests he advanced at the head of his men, wildly waving his sword in encouragement when he was fatally hit on August 29, 1862.

He left behind a wife, Ann Eliza Abbot, and one daughter, Ada Frances.

Abbott is buried in Riverview Cemetery in Trenton, New Jersey.