Dundee services currently fly into London City while Derry flights operate to Stansted. These will shift to Heathrow Terminal 2 early next month.
Single-ticket connections from Derry through Heathrow range to 119 destinations across 56 countries, while from Dundee there are 97 options across 45 countries.
In addition, Scottish island services via Dundee – from Kirkwall airport in the Orkney Islands and Sumburgh airport in the Shetland Islands – will also now fly into Heathrow.
Loganair described the shake-up as "the largest single expansion of regional, domestic air connectivity at Heathrow in a generation".