Allen received his early education from Presbyterian ministers and from John S. McNamara, considered in his day an exceptional mathematician. In 1819 he studied law at Transylvania University, and later practised for a short time in Bloomington, Indiana.
Allen entered the army before he was seventeen years old and served six months in a Virginia regiment. In 1816, while he was riding through a forest, lightning struck a tree, which fell, killing a young woman riding with him, crushing his own horse, and so injuring him that thereafter his left arm was practically useless.
Coming under the influence of Barton W. Stone, however, he was converted to the religious views of that leader, was baptized by him in 1823, and returned to Kentucky, where in 1825 he was ordained by Stone at "Old Union" Church, Fayette County, which Allen and five others had established two years before. Soon he was prominent in the councils and activities of the Christians, and planted churches of that order in Paris, Antioch, Clintonville, and Cynthiana. He was one of those instrumental in bringing about the union between the followers of Stone and those of Alexander Campbell which was effected in 1832.
In 1836 he removed to Boone County, Missouri. There he possessed ample means and the farm which he purchased, worked by slaves so well cared for that the most of them remained with him after the emancipation, became one of the best estates in the county.
Allen was frequently urged to become the Whig candidate for governor, and declined an appointment to Congress to fill an unexpired term. Although a slave-holder, he was opposed to secession, and at a meeting of citizens of Boone County, held May 6, 1861, he urged them to maintain an armed neutrality within the Union, and not be driven away by passion and prejudice into the dangerous experiment of revolution and anarchy.
His chief interest always was the extension of religion and education, and to this he gave himself untiringly almost to the day of his death. He went where there were no churches, preaching in court-houses, schoolhouses, barns, and groves.
Allen was a member of the first board of curators of the University of Missouri, and president of the board in 1839, 1841, and again in 1864; and a member of the governing board of Christian Female College.
Allen actively served as a preacher of the gospel until the fall of 1871. He died on October 10, 1871, in Columbia, Missouri.
Allen was six feet tall, of commanding person, always dressed in faultless taste, an easy speaker, and an accomplished gentleman. He was a person of extensive influence; his home was noted for its hospitality, and he was intimate with the leading men of the state.
In 1819 Allen married Rebecca Russell of Fayette County.