Most captured B-17s were given high visibility German national markings and used for the training of fighter pilots in the development of tactics that would be effective against USAAF-operated Fortresses. However, some were flown in their original USAAF markings for various clandestine purposes such as sneak penetrations of Allied territory, the dropping of agents, or the supplying of secret bases. The most well-known Luftwaffe unit to operate the captured B-17 in such a fashion was the notorious I/K.G.200. The exploits of I/K.G.200 are sort of shadowy and not much is written about this outfit in most histories of World War 2. One of their better-known exploits took place in the spring of 1944 in the Western desert (long after Rommel had been run out of Africa) and involved the use of captured B-17s and other Allied aircraft for the construction and maintenance of a series of secret airstrips and fuel dumps. A captured Fortress was used to parachute agents into Jordan in October of 1944. In Luftwaffe service, the B-17 was assigned the cover designation of "Dornier Do 200".

There are reports that at least one captured B-17 was used by the Luftwaffe as a decoy. It would follow returning USAAF B-17 formations, pretending to be a crippled straggler and hoping to draw a B-17 out of the formation to cover it against fighter attack during the flight home. Once the protective B-17 closed in, the decoy would fire at it with its own guns or would call in German fighters to finish it off. This practice was enough of a threat that USAAF bomber formations would often fire upon an approaching straggler that could not be positively identified.

In the Pacific theatre, most USAAC B-17s were destroyed on the ground during the first few days of the war. However, the Japanese advance was so rapid that Allied forces were often forced to leave some of their aircraft behind as they retreated. As a result, the Japanese forces managed to obtain a collection of different types of Allied aircraft that they were able to put back into the air with fairly little effort. The Japanese obtained at least three Fortresses--two B-17Ds and one early B-17E--which were flown to Japan for use in a public display of captured enemy aircraft. These captured B-17s were used for careful evaluation of their capabilities and the development of fighter tactics against them.