In 1967, Loganair took delivery of three Britten-Norman Islander twin-engine eight-seat light commuter airliners and began regular flights between the Orkney Islands, and started operating in Shetland in 1970. In 1966, after Renfrew Airport closed, the airline established its head office at Glasgow Airport. This aspect of Loganair's operations ceased on 31 March 2006 when the new contract for air ambulance work was awarded to Gama Aviation.
In 1993, the airline became a franchisee of British Airways, operating its Islanders in the British Airways livery. This would stand until July 2008, when it became the new franchisee of Flybe.
After a restructure of British Midland Group in 1994, Loganair's routes outside Scotland and the aircraft used to operate them were transferred to Manx Airlines. This consolidation of services led to the formation of a new airline, British Regional Airline (BRA Ltd). In 1997, with Loganair now consisting of six aircraft (one de Havilland Canada DHC-6 Twin Otter and five Britten Norman Islanders) and 44 staff, a management buy-out occurred.
Operations as Flybe franchisee and later developments
In June 2005, Loganair was awarded a contract from the Irish Government to operate a daily return service from Knock, County Mayo to Dublin. This public service obligation (PSO) route operated for a period of three years as British Airways, with effect from 22 July 2005. The operation ceased in July 2008, the contract having been lost to Aer Arann. The airline also bought routes from Citiexpress in March 2004.
Until October 2008, Loganair was a British Airways franchisee, operating flights sold through BA using BA flight codes. Loganair's inter-island operations between the Orkney and Shetland Islands carried out using Britten-Norman Islanders were removed from the franchise agreement in 2004. The flights have since been marketed under Loganair's own name, rather than British Airways'. Loganair became a franchise airline of Flybe, operating in the Flybe colours. Flights are also operated under a codeshare agreement with British Airways connecting flights from Scotland to London. The franchise has been criticised by residents in the Scottish islands for what they perceive to be excessively high fares, and a Facebook campaign set up in June 2015 to highlight the issue attracted over 7400 "likes" over the course of its first weekend.
On 8 July 2011, it was announced that Loganair had agreed to purchase Cambridge based ScotAirways. ScotAirways continued to trade as a separate entity (using its original name of Suckling Airways) and holding its own licences and approvals until April 2013.
On 21 November 2016, Flybe and Loganair announced that their franchise agreement would terminate on 31 August 2017. Despite headlines, it is unclear who initiated the termination. Loganair later relaunched its website without renewed interline agreements with Flybe or Aer Lingus.
In April 2017, pending the termination of the Flybe franchise agreement, Loganair unveiled its new independent corporate livery on Saab 340B Freighter G-LGNN. From 1 September the airline began operating "in its own right" for the first time in 24 years. Loganair signed a codeshare agreement with British Airways (BA), effective from 1 September 2017 (coinciding with the launch of independent operations), allowing passengers to book through flights onto BA's global network.
Reactions to the demise of other airlines
In February 2019, following Flybmi's cessation of operations, Loganair announced that it was to take over Flybmi's routes from Aberdeen to Bristol, Oslo and Esbjerg, from Newcastle to Stavanger and Brussels, and from City of Derry Airport to London-Stansted.
In March 2020, following Flybe's cessation of operations, Loganair announced that it was to take over the following Flybe routes from Scotland and Newcastle: Aberdeen-Belfast City; Aberdeen-Birmingham; Aberdeen-Jersey; Aberdeen-Manchester; Edinburgh-Cardiff; Edinburgh-Exeter; Edinburgh-Manchester; Edinburgh-Newquay; Edinburgh-Southampton; Glasgow-Exeter; Glasgow-Southampton; Inverness-Belfast City; Inverness-Birmingham; Inverness-Jersey; Newcastle-Exeter; Newcastle-Southampton 
As of September 2019[update], Loganair serves 44 destinations in the United Kingdom, Channel Islands, the Isle of Man, the Republic of Ireland and Europe. Part of Loganair's operations includes the world's shortest scheduled commercial route, between Westray Airport and Papa Westray Airport, a distance of 1.7 miles, and the use of Barra Airport, the only airport in the world to use a beach as a runway.
With the collapse of the airline Flybe in March 2020, Loganair took over a number of former Flybe routes from Scotland and the North of England, with service beginning as little as 10 days after the collapse of Flybe.
Loganair has codeshare agreements with the following airlines (as of July 2020):
In June 2018, it was announced that Loganair plan to add at least a further two Embraer ERJ-145 aircraft for the start of the summer 2019 schedule. The aircraft are to be transferred to Loganair from its sister company Flybmi and will initially be used to operate flights from Loganair's Glasgow base to Derry and Stornoway. Loganair plan to eventually use the Embraer ERJ-145 aircraft to launch new routes to European airports that are currently not served from Glasgow.
Loganair is planning to introduce electric aircraft to the Orkney Islands by 2021 due to the short distance between the islands that would make such flights possible.
Loganair has continued to follow its fleet simplification programme through 2019 by phasing out the small subfleets of Dornier 328 and Saab 2000s to focus on the Saab 340 and Embraer ERJ families in the near term before the gradual phase in of the ATR 42 fleet. By April 2019, the D328 fleet had already been Withdrawn From Use (WFU) and stored.
Loganair returned the last of their Saab 2000 aircraft to the lessor on 25 March 2020
On 12 June 1986, a DHC-6 Twin Otter aircraft with 16 people on board struck high ground on the island of Islay in poor weather. The pilots had mistakenly identified the coastal village of Laphroaig as the town of Port Ellen, near Islay's Glenegedale Airport. There was one fatality, a pilot.
In 1996, a Britten-Norman Islander was destroyed in Shetland. The accident occurred during a night time return flight to the aircraft's home base following a medical evacuation flight. The aircraft crashed short of the runway whilst attempting to land after a previous discontinued approach in strong gusting cross winds. The pilot had exercised his discretion to extend the period for which he was allowed to fly that day. The pilot's medical certificate had expired nineteen days earlier thus invalidating his pilot's licence. The pilot was killed in the crash and a doctor on board was seriously injured; a nurse seated at the rear of the aircraft sustained minor injuries.
On 27 February 2001, Flight 670 a Short 360 registered G-BNMT operating a Royal Mail flight to Belfast, crashed into the Firth of Forth shortly after taking off from Edinburgh at 1730GMT. Both crew members were killed, but there were no passengers on board. An Air Accidents Investigation Branch (AAIB) inquiry later blamed a buildup of slush in the aircraft's engines for the crash. Protective covers had not been fitted to the engine intakes while the aircraft was parked for several hours in heavy snow at Edinburgh.