On 6 September 1930 Mahoney joined the Royal Marines at Plymouth as a Boy Bugler age fourteen and a half. His Regimental Number was: Plymouth/X 564. He joined HMS Exeter as a bugler but on 31 January 1933 transferred to the General Duty Branch as a Marine and in May 1933 was drafted to Deal, Chatham and Plymouth for infantry and gunnery training. He then joined HMS Dorsetshire from April 1935 to 14 June 1937 and was promoted to Corporal on 27 August 1937. The next year he volunteered for flying training and on 8 October 1939 was transferred to the RN on probation as an Acting Leading Seaman to join No 7 Naval Pilots Course. The other Royal Marine on his course was Lieutenant H M H Edwards. His Elementary Flying Training took place at Sydenham, Belfast, before graduating to No 7 FTS at Peterborough and he finally qualified as a pilot on 27 May 1940. The next day he was promoted to Acting Petty Officer Airman and immediately commenced fighter pilot training at RNAS Eastleigh.

After qualifying as a fighter pilot flying Gladiators he joined 804 Squadron at RNAS Hatston from 18 July and together with Lieutenants Marsh and Wright, also in the squadron, was awarded the Battle of Britain Clasp to his 1939-1945 Star. In November 1940 he was drafted back to RNASs Yeovilton and Eastleigh for refresher training, but, thereafter, did not fly fighters again. Instead, in May 1941 he joined HMS Edinburgh Castle for 777 Squadron. Edinburgh Castle was the base depot ship at Freetown, Sierra Leone, and 777 Squadron was formed at Hastings, Sierra Leone, on 1 August 1941 as a Fleet Requirements Unit. The squadron was initially equipped with Swordfish and Rocs, to which were added Defiants and several Walruses during 1942. 

Mahoney returned to RNAS Yeovilton briefly for 790 Squadron on 28 September 1942 before joining HMS Blackcap, RNAS Stretton, for 776 Squadron from 25 November 1942 until 1 May 1944 during which he attended a twin engine conversion course. In May 1944 Mahoney returned again to Lee-on-Solent for an Upper Yardman Course and on 12 January 1945 was promoted to Sub-Lieutenant. Newly promoted, he was appointed to HMS Kestrel, RNAS Worthy Down, for ferry pilot duties from 17 January to 13 March 1945 before being posted to RNAS Arbroath (additional), from 14 March to 30 May 1945 to attend a flying instructors course at No 2 FIS, Montrose, flying Harvards.

As a newly qualified instructor he returned to Lee-on-Solent for instructional duties in 798 Squadron from 6 June to 5 September 1945 and promoted to Acting Lieutenant. From Lee-on-Solent Mahoney joined HMS Godwit, RNAS Hinstock, the FAA's Advanced Instrument Flying School for instructional duties in 758 and 780 Squadrons during which he completed the Advanced Instrument Instructors Course and on 27 November 1946 was promoted to Lieutenant.

From RNAS Hinstock he was appointed briefly to HMS Jackdaw, RNAS Crail, and then on to HMS Condor, RNAS Arbroath, from 24 March 1947 to 30 June 1947 as the Senior Pilot of No 4 Ferry Flight and also as the instructor converting pilots to fly twin-engned Oxfords.  From Condor Mahoney then joined HMS Fieldfare, RNAS Evanton, from 1 July 1947 to 30 March 1948 for its Station Flight and as Assistant to the Lieutenant Commander Flying. From Fieldfare he was appointed to RNAS Donibristle, (additional), as an exchange instructor at RAF Syerston until June 1949 instructing on both Harvards and Tiger Moths.

On completion of his exchange tour, Mahoney then joined HMS Fulmar, RNAS Lossiemouth, for 766 Squadron from 17 June 1949 to 11 March 1950 as the officer in charge of instrument training. Unfortunately, for administrative reasons, his time in RNAS Lossiemouth was short lived and he moved to HMS Gannet, RNAS Eglinton from 26 April 1950 to 3 April 1951 for instructional duties in 815 Squadron flying Barracudas, Fireflys and Deck Landing Training on HMS Vengeance. He returned to RNAS Lee-on-Solent 4 April 1951 to 8 May 1953 for 781 Squadron as a member of the Instrument Flying Examining Flight, flying Barracudas, Fireflys and Oxfords. He received an above average report and was upgraded to A.2 instructor before being appointed to HMS Helmsdale, a River class frigate to gain his watchkeeping certificate. He was promoted to Lieutenant Commander on 1 January 1954.

From Helmsdale Mahoney was appointed back to RNAS Eglinton, for 719 Squadron flying Fireflys by which time he was recognised as an experienced instructor having by then having flown over 3800 hours, held an A 2 flying instructors category and a Master Green instrument rating. From Gannet he joined HMS Peregrine, RNAS Ford, for 771 Squadron until 22 June 1956 and during that tour he did a short attachment back to Gannet for a Gannet aircraft conversion course after which, back at Ford, he was lent as an instructor on Gannets to the Channel Air Division RNVR until 22 June 1956.

Mahoney's next and final appointment was to HMS Seahawk, RNAS Culdrose, for 750 Squadron as a twin conversion instructor and, by then, he had also qualified as an Instrument Grading Examiner. During this tour he was lent to 796 Squadron converting Firefly pilots to fly the Gannet and was also in charge of the Devon Flight. After his brief experience in fighters, Mahoney built up a wealth of experience on many aircraft types and clearly had a particular aptitude as an instrument flying instructor. He was placed on the retired list on 29 July 1958.