Under Methodist influence Henry Allon decided to enter the ministry, but, developing Congregational ideas, was trained at Cheshunt College, Hertfordshire and became closely associated with the Union Chapel in Islington. For a short while, he was co-pastor at the Union Chapel with the Rev. Thomas Lewis (1844–1852), but thereafter sole pastor for forty years (1852–92). During this time he gained considerable influence amongst metropolitan Congregationalists and secured the funds required for an ambitious rebuilding programme at the Union Chapel, between 1874 and 1890, from designs by James Cubitt.
In 1865, Allon became co-editor with Henry Robert Reynolds of the British Quarterly Review, and in 1877, the sole editor of that journal for another ten years. He published Memoir of the Rev. J. Sherman in 1863, Life of William Ellis in 1873, and sermons on The Vision of God in 1876. Only one hymn is attributed to him, Low in Thine Agony (1868), but he published numerous musical compilations, and his son Henry Erskine Allon was a composer (1864–97).