Allen was born in Northampton, Massachusetts on 17 October 1743. His parents were Samuel Allen (1706–1755) and Hannah Miller (1707–1755). Allen married Lydia Richards (1746–1833) in 1762 in New Marlborough, Massachusetts. She was the daughter of Zebulon Richards and Lydia Brown.
Along with Thomas Ashley, Allen was a founder of Poultney, Vermont. Allen and Ashley (both had married daughters of Zebulon Richards) arrived at the site of the town along the Poultney River on 15 April 1771. Allen brought his family with him on the journey. Ashley traveled alone, building a shanty and planting corn before bringing his family to the wilderness.
Allen became a Lieutenant in a company of Green Mountain Boys, was with Ethan Allen when Ft. Ticonderoga was captured from the British, and with Colonel Warner in Canada. He was appointed a captain in Colonel Herrick's battalion of rangers in July 1777, and distinguished himself at the battle of Bennington. In September of the same year he captured Mt. Defiance by assault, and on the retreat of the enemy from Fort Ticonderoga made fifty of them prisoners. Subsequently he was made major in the rangers, and showed himself a brave partisan leader. In his later life he was always referred to as Col. Allen.
Allen occupied many positions of civil authority in Vermont. He was a Justice of the Peace, served on many town committees, and was a representative to the Vermont General Assembly from 1788-1792. He was prominent in the planning of a new government for Vermont, helping to frame its constitution.
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 25 August 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 - 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.
Allen was known as a man of strong convictions—whether political, moral or religious. He was opposed to slavery. On 27 November 1777, he granted freedom to two slaves stating: "I being conscientious that it is not right in the sight of God to keep slaves, give them their freedom."
In 1792 Allen toured the unsettled portions of Ohio, Michigan and Upper Canada with a group of Indians for a year. In 1795, Allen was part of a partnership with Charles Whitney, also of Vermont, Robert Randal, of Philadelphia and several British subjects in Detroit including John Askin and William Robertson, which planned to buy the entire lower Michigan peninsula from the United States government for $500,000. A stock company was established, and two of Allen's eastern partners promised members of Congress either stock or cash for their support in the purchase. This clumsy scheme was exposed, and the partner's plans evaporated.
Ebenezer, or “Indian,” Allan was from many angles a dramatic and certainly a colorful figure-a man well suited to carry out the purpose of building a new frontier millsite in a mill-site newly acquired "West of The Genesee River" in what is now Rochester New York. He was chosen to carry out this task by developer Oliver Phelps. Although as a Tory ranger he had earned a bad reputation among the settlers to the south and east, Allan had later operated for several years as a peaceful trader among the Indians along the Genesee River. He had two daughters by a Seneca wife, and his enterprising activity had made him a figure of some importance in the Indian community. Allan had proved agreeable to the Phelps and Gorham purchase in the summer of 1788, and before returning to New England Oliver Phelps chose this hardy frontiersman as the man to build and operate the mills at the falls of the Genesee in what would become Rochester New York. It is uncertain whether the One-Hundred-Acre Tract was given as a reward for his co-operation in bringing the Indians to terms at Buffalo Creek, or as an inducement for Allan to undertake the expense of building the mills on such a distant and unsettled frontier. In any case, title was promised by the following Articles of Agreement On 30 Sep. 1788: N. Gorham and O. Phelps & Co., by their agents Wm. Walker, Caleb Barton and Benj. Barton articled to Ebenezer Allan the privilege of a grist mill and saw mill with lands sufficient for mill yards and roads to the same and likewise 100 acres of land adjoining the same; provided the said lands shall not interfere with or injure any carrying place, ferry or town plat which may hereafter be found advantageous to the Company. Always reserving one half of all mines and minerals which have or may hereafter be found on said lands, and to build a good grist mill and saw mill by the 1st of June next. Allan may have doubted the possibility of making his mills a vital link between the Indians and the white men, for, Indian trader though he was, he had recently married Lucy Chapman, a white woman, thus aligning himself more definitely with the settlers’ frontier. Indeed, Allan had already partially cleared and improved a farm of 472 acres near the site of present Scottsville, and most of his few neighbors were his own relations, either by blood or marriage. Lucy’s parents and her sister, married to Nicholas Miller, all resided in the vicinity, as did Allan’s own sister and her husband, Christopher Dugan. Other settlers began to arrive in 1789, founding Canandaigua, Bloomfiield, Hartford [Avon], and Northfield [Pittsford] -to mention but a few of the pioneer communities. Allan was able to sell his Scottsville farm to Peter Shaeffer late that year for $2.50 an acre, a very good price for that day. Doubtless the prospect of an active trade with the growing settlements prompted Allan to transfer most of his interest to the millseat at the falls of the Genesee- thus taking his stand at an extreme outpost of the Genesee frontier. Allen build his mills but after a few years they proved to be unsuccessful. He sold his 100 acre tract in 1792. The deed passed through many people before it was purchased by Nathaniel Rochester in 1803 and the future city of Rochester NY was born.
Ebenezer Allen married Lydia Richards and they had 8 children : 1. Abiel Allen (1763 in Poultney - 1765 in New Marlborough, MA) 2. Timothy Allen (1765 in Poultney - 1850 in South Hero) 3. Mary Allen (1766 in Vermont - ? in Vermont) 4. Lydia Allen (1768 in Poultney - 1800 in ?) 5. Ebenezer Allen Jr. (1771 in South Hero - July 2, 1844 in LaPorte, Indiana) 6. Amy Allen (1775 in Poultney - April 30, 1822 in South Hero) 7. Charlotte Allen (1777 in South Hero - September 13, 1813 in South Hero) 8. Eunice Allen (April 7, 1779 in Tinmouth - Jan. 24,1852 in Rome, Michigan)
- Smith, Henry P. & Rann, William S., The History of Rutland County, Vermont, Syracuse: D. Mason & Co., 1886
- Joslin, Joseph, "A History of the Town of Poultney, Vermont, from its Settlement to the Year 1875", Poultney: Journal Printing Office, 1875
- Hemenway, Abbey, "The Vermont Historical Gazetteer", (Clark, History of South Hero), Burlington: The Author, 1871, vol. II, p. 580-81
- Hemenway, Abbey, "The Vermont Historical Gazetteer", Burlington: The Author, 1871, vol. II, p. 582
- Hemenway, Abbey, "The Vermont Historical Gazetteer", Burlington: The Author, 1871, vol. II, p. 573
- Joslin, Joseph, "A History of the Town of Poultney, Vermont, from its Settlement to the Year 1875", Poultney: Journal Printing Office, 1875, p. 198
- "Account of a Plot for Obtaining the Lower Peninsula of Michigan from the United States in 1795 by J. V. Campbell". Collections of the Pioneer Society of the State of Michigan together with Reports of County Pioneer Societies, Vol VIII (second ed.). Lansing, Mich.: Wynkoop Hallenbeck Crawford. 1907 . pp. 406–411. Retrieved 2006-10-15.
- "Col Ebenezer Allen". Find A Grave. Retrieved September 26, 2012.