Although it had many advanced features, the Me 309's performance left much to be desired and it had so many problems that the project was cancelled with only four prototypes built.

Messerschmitt's failure to resolve the stability and other problems of the Me 209 project during 1940 caused Willy Messerschmitt to scrap much of the earlier design work when he commissioned wind tunnel testing of new wing designs and the cockpit canopy in January 1941.

Low government interest in the project delayed completion of the first prototype until spring 1942, and trouble with the nosewheel pushed back the 309's first flight to July.

When it did fly, the Me 309's performance was satisfactory – about 50 km/h (30 mph) faster than a standard Bf 109G – but not exemplary.

Two versions were planned: a heavy fighter with four or six 30 mm MK 108 cannon, and a Schnellbomber (Fast bomber) variant with two 30 mm MK 108 cannon and a bombload of 1,000 kg (2,200 lb) carried beneath the fuselages.