In the middle of 1940 Messerschmitt started the design of what was to be the successor of the 109. The new fighter was to have a retractable tri-cycle undercarriage, a variable geometry radiator and off-coarse more speed and firepower than the 109. At the end of 1941 the detail design was finished and the RLM assigned the number 309 to the new fighter. Priority was low however because there was no sense of urgency at the RLM for finding a successor to the 109.

A number of Me-109F test airframes were assigned to the 309 program to test various features of the new design. The V-23 was used to test the new ventral radiator, the V-31 to test both the radiator and the tri-cycle undercarriage and the V-30 for the testing of the cabin pressurization system.

Meanwhile the interest from the side of the RLM  gradually declined. Nevertheless the construction of the first prototype progressed and the V-1 was completed in June 1942. Trouble with the nose wheel during taxiing trials delayed the first flight until the end of July. After some initial problems with the radiator and the reversible pitch airscrew the tests preceded favorable.

Tests at Rechlin confirmed that the Me-309 could be made into a fighter but offered little improvement in performance over the Me-109G which could also out turn the Me-309. At this time the introduction of new, better fighters like the FW-190D was near and little use was seen for the Me-309.

In all four prototypes were produced. The V-4 was armed with four MG 131, two MK 108 and a MG 151/20. This heavy armament led to a decrease in speed that was unacceptable for a fighter. In the autumn of 1943 the Me-309 program was officially terminated. 

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The base for this model was Col. Gibbons HR ME109K.