On 1 January 1941 Germany began negotiations with Bulgaria to allow German troops to use Bulgaria as a base for the planed attack on Greece. On 2 March 1941, one day after Bulgaria signed the Axis Tripartite Pact, the German 12th Army and Fliegerkorps VIII began to deploy inside Bulgaria. A number of aircraft were also supplied from Germany, and Luftwaffe advisors and instructors were attached to Bulgarian squadrons. Operation Marita, the German attack on Greece and Yugoslavia began on 6 April 1941. Bulgarian forces did not participate in the attack, but took up defensive positions to counter possible retaliation. A few air raids by Yugoslav and RAF bombers were carried out before the rapid German advance over-ran enemy air bases.
In late April 1941, Bulgarian ground and air forces moved into Macedonia and Aegean Thrace, as these areas now fell under Bulgarian administration. Numerous reconnaissance sorties were flown over the Aegean to track enemy shipping. In the summer, the aircraft strength along the Black Sea coast was boosted, as the German invasion of Soviet Union had not affected the offensive capabilities of the Soviet Black Sea Fleet.
Early 1942 was relatively calm, apart from some high altitude reconnaissance flights by British and US aircraft. Anticipating future developments, a request for night fighters from Germany was denied. From June 1942 North African based USAAF bombers began raiding the Ploesti oil refineries in Romania. The aircraft passed through Bulgarian airspace, dropping a few bombs on the way.
The increasing threat from air raids forced a re-appraisal of air defences. Existing fighter aircraft were of a diversity of types and, apart from the Messerschmitt Bf 109E, increasingly obsolete. Serviceability was also very poor due to lack of spares. Accordingly, a batch of Bf 109G and Dewoitine D.520 fighters was delivered in 1943, together with the deployment of the first radar units for the Air Warning Service. Luftwaffe fighter units based in Bulgaria were now increasingly needed on the Russian front, and so Bulgarian fighter squadrons had to assume a larger air defence role.
Operation Tidal Wave, a massed air raid by American B-24 Liberators on 1 August 1943 was intercepted by Bulgarian fighters as it headed towards Romania. The Royal Bulgarian Air Force was now able to claim its first aerial victories, with Bf 109G pilots managing to bring down four B-24s. 14 November 1943 marked the start of a series of nine daylight air raids on the Bulgarian capital, Sofia. A late warning hindered the defences and only one escorting P-38 was shot down. Subsequent raids were heavier and involved aircraft from the Italian-based US 15th Air Force as well as the North African-based 9th Air Force. Bulgarian air defences became increasingly well organised, but despite fierce fighting could only bring down and average of 2% of the enemy raiders (39 aircraft in total) for the loss of 14 of their own. Eight night raids were also staged, but the lack of night fighters and night flying skills left aerial defence to the anti-aircraft artillery. After April 1944 the Allied bomber offensive returned to attacking Ploesti, with only sporadic air engagements occuring over Bulgaria.
As the advancing Soviet Army approached Bulgaria's borders in August 1944, German troops began pulling out. The last German units left on 30 August 1944. The following week Bulgaria allied itself with the Soviet Union and began preparations to fight alongside the Red Army against Germany. Between 9 September and 7 October 1944 the Bulgarian Air Force flew more than 1200 sorties against German forces, in preparation for a ground offensive which began on 9 October. Support for the ground offensive was mainly provided by the Soviet 17th Air Army, as the serviceability of German-supplied aircraft began to decline rapidly. Combat operations ceased on 2 December 1944 with the liberation of Southern Serbia. In 1945 the first Soviet aircraft began to enter service, reflecting the new political orientation of the country.