Allen was one of the original grantees of South Hero, Vermont by an act of the legislature in 1779. He left Poultney with his family for South Hero, Vermont where he once again was the first pioneer in a wilderness—tradition states that he arrived on August 25, 1783, however he may have arrived as early as 1779. In 1787 he enlarged his house and operated a public house on the island. He held many public offices and was a representative to the Vermont General Assembly from 1788 to 1792. His cousin, Ethan Allen, spent the last night of his life at his house in South Hero. Ebenezer removed from South Hero to Burlington, Vermont in 1800 and operated a tavern there until his death in 1806.