After leaving Yale, Ebenezer arrived in Boston, where he received an appointment as a first lieutenant in Captain Chester's Company of General Joseph's 2nd Connecticut Regiment. He participated in the Siege of Boston until its close, when he marched with General Washington to New York. In May 1776, he was promoted to captain and fought in the Battle of Long Island on August 27 under Colonel Samuel Wyllys. By the end of the battle, he was promoted to brigade major under Brigadier General Samuel Holden Parsons. The regiment suffered significant casualties in Long Island.