At the opening of the College of Science on 8th July 1911, Deane was knighted by King George V.^[1] On 3rd May 1915, Lieutenant Thomas Alexander Deane, his son was killed in action at Gallipoli. After his only son's death, Deane resigned from the Royal Institute of the Architects of Ireland and agreed to very little further architectural work. In his later years, the most significant buildings that he worked on were the Reading Room at Trinity College and the War Memorial Hall.^[2]

Around 1925 he retired to Wales along with his wife, Florence Mary (née Wright). They relocated to the town Penmaenmawr, which is on the North Wales coast.^[1] Toward the end years of his life, Deane’s eyesight began to deteriorate.^[2] He died at Erw-Lyden, North Wales on 3rd February 1933.^[3] He was 81 years old. He left an estate of £4,647 to his wife and his daughter, Mrs. Mary Primrose Thorp.^[2]

Many of Thomas Manly Deane's sketchbooks and drawings, some dating back to the time he spent in Italy from 1877-1878, and the diary he wrote while on a visit to Spain and France in September of 1880 are held in the National Gallery of Ireland. An album titled ‘Own works, all designed by T. Manly Deane’ containing hundreds of photographs and architectural drawings of buildings and furnishings composed by Deane is in the National Library of Ireland.^[2]