[5] It holds a United Kingdom Civil Aviation Authority Type A Operating Licence, permitting it to carry passengers, cargo and mail on aircraft with 20 or more seats.

[12] After a restructure of British Midland Group in early 1994, Loganair's routes outside Scotland and the aircraft used to operate them were transferred to Manx Airlines.

[16] In 1997 a management buy-out occurred with Loganair becoming independent of BRAL and operating just six aircraft (one de Havilland Canada DHC-6 Twin Otter and five Britten Norman Islanders) with 44 staff.

The franchise has been criticised by residents in the Scottish islands for what they perceive to be excessively high fares,[20][21] and a Facebook campaign set up in June 2015 to highlight the issue attracted over 7400 "likes" over the course of its first weekend.

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.

[26] In May 2015, two Viking Air DHC-6-400 Twin Otter aircraft were acquired by Highlands and Islands Airports to be operated by Loganair on the Scottish Government's Public Service Obligation routes between Glasgow and Campbeltown, Tiree and Barra.

[31] In April 2017, pending the termination of the Flybe franchise agreement, Loganair unveiled its new independent corporate livery on Saab 340B Freighter G-LGNN.

[36] A BALPA tribunal into Loganair's swift action following the closure of Flybmi found that the carrier had been acting lawfully, despite the fact that it had created several contingency plans for the demise of UK airlines Eastern Airways and Flybe.

[40] As of September 2019[update], Loganair serves 44 destinations in the United Kingdom, the Isle of Man, the Republic of Ireland and continental Europe.

[43] In March 2023, Loganair secured a lease from British Airways for 30 additional slot pairs at Heathrow, previously leased to the relaunched Flybe before its demise in January 2023, and called on the UK government to reform competition remedies in order to ensure that Heathrow slots remain permanently available for UK regional connectivity.

The aircraft were to be transferred from sister company Flybmi, and would initially operate flights from Loganair's Glasgow base to Derry and Stornoway.

[67][68] In January 2024, Loganair announced plans to introduce a hydrogen fuel cell-powered Britten-Norman BN-2 Islander on its Orkney island-hopping routes by 2027.