The Fleet Air Arm handed the Station back to the Royal Air Force on 28 September 1972 and D Flight, 202 Squadron, the Helicopter Search and Rescue Flight, was the first RAF unit to return. May 1973 saw the arrival of the Jaguar Conversion Team (renamed 226 Operational Conversion Unit on 1 October 1974) and in August 1973, 8 Squadron Shackletons transferred to Lossiemouth from nearby Kinloss. In December 1978, 48 Squadron of the Royal Air Force Regiment arrived to provide short-range defence with their Rapier surface-to-air missiles. In July 1979, 2622 (Highland) Royal Air Force Auxiliary Regiment was formed, tasked with the ground defence of the Station. From 1978 to 1981, 2 Tactical Weapons Unit flew Hunters from Lossiemouth prior to the reopening of RAF Chivenor. On 1 July 1991 the Shackletons of 8 Squadron retired from service and on 1 October 1991 237 Operational Conversion Unit was disbanded. In 1992 however, another unit was added to the Station strength with the formation of 237 Field Squadron of the Territorial Army responsible for Airfield Damage Repair. Also during that year, the important links between RAF Lossiemouth and the District of Moray were further strengthened when the Station formally received the Freedom of Moray.
Major changes took place in 1993 with the Buccaneer anti-shipping squadrons starting to be replaced by the Tornado. On 1 October 12(B) Squadron lost its Buccaneers but kept its squadron number-plate when re-equipped with Tornados. On 1 November, the Tornado Weapons Conversion Unit, renamed XV(Reserve) Squadron arrived from RAF Honington in Suffolk.
In April 1994, 208 Squadron was disbanded and was replaced by 617 Squadron, which transferred with their Tornados from RAF Marham in Norfolk. Although 48 Squadron Royal Air Force Regiment left Lossiemouth for Honington on 1 July 1996, RAF Lossiemouth continued to be one of the busiest front-line stations in the RAF with 3 Tornado Squadrons, including XV(Reserve) Squadron, 16(Reserve) Squadron (previously 226 OCU) and D Flight, 202 Squadron with their Sea Kings. This line-up continued until July 2000, when the Jaguars left for RAF Coltishall in Norfolk; however, with the increase in size of XV(Reserve) Squadron in 1999 following the closure of the Tri-national Tornado Training Establishment at RAF Cottesmore, the arrival of the Tornados of 14 Squadron from RAF Brüggen in January 2001, RAF Lossiemouth has become the busiest fast-jet station in the Royal Air Force. In May 2001, 51 RAF Regiment Squadron was reformed and now sits with 2622 Auxiliary Squadron under the newly formed 5 Force Protection Wing Headquarters at RAF Lossiemouth.