After spending a little over three years in command of the composite screw sloop Wanderer, Allenby was promoted to the rank of Commander on 1 January, 1897.
On 31 December, 1902, Allenby was promoted to the rank of Captain. He was appointed to President, additional, for service at the Admiralty on 21 May, 1903, and on 16 June was appointed Naval Attaché to Germany, Denmark and the Netherlands. On the occasion of the King's visit to Copenhagen he was appointed a Member of the Fourth Class of the Royal Victorian Order (M.V.O.) on 18 April, 1904.
Superseded as Naval Attache on 9 February, 1906, he was appointed in command of the battleship Centurion on 19 February. On 6 March he was lent to the War Course, where he was rated First Class and "Good."
He was appointed in command of the armoured cruiser Argyll on 12 March, 1907, being superseded in her on 24 March, 1909. He took command of the battleship Formidable on 20 April, and was superseded in command on 4 April, 1911. He was then appointed Captain of the dreadnought battleship Temeraire on 12 August.
Allenby was promoted to the rank of Rear-Admiral on 20 March, 1913, vice Pelham. He was superseded in command of Temeraire on 5 April, and on 18 August was appointed to a Signal Course. He attended the Royal Naval War College at Portsmouth from 8 September to 19 December, and was placed second out of three flag officers in order of merit. The President, Vice-Admiral The Honourable Sir Alexander E. Bethell, commented that "He has done very well." From 2 February to 13 March, 1914, he took Gunnery and Torpedo Courses.
In accordance with the provisions of the Order in Council of 8 December, 1903, Allenby was placed on the Retired List, at his own request, on 18 February, 1915. On 11 April he was appointed temporary Lieutenant-Colonel as an Assistant Embarkation Staff Officer.
Allenby was appointed as Principal Naval Transport Officer, Egypt on 2 February, 1916 and assumed his duties on 25 February. On 9 July, he reported that he had had to go to hospital for observation, but he was back on duty on 15 July. He continued to serve as P.N.T.O., Egypt until 22 February, 1917 and was sent home, arriving on 3 March, 1917.
Special service on the books of President occupied him until July, 1917 when he was to hoist his flag in the commissioned escort ship Quernmore, but she was sunk by U 82 northwest of Ireland on 31 July, thankfully with the loss of just one man.
Allenby was appointed to the newly-commissioned escort ship Wyncote from 8 September 1917 until March, 1918.
On 1 January, 1918, he was appointed a companion of the Distinguished Service Order. He was advanced to Vice-Admiral on the Retired List on 20 January, 1918, and to Admiral on the Retired List on 5 July, 1921.