The bomber was field tested in the Spanish Civil War, where it proved inferior to the Heinkel He 111. Four Ju 86D-1s arrived in Spain in early February 1937, but after a few sorties one of them was shot down on 23 February by Republican fighters with the loss of three crewmen killed and one captured. A replacement aircraft was sent from Germany, but in the summer of 1937 another was lost in an accident, and the three remaining aircraft were sold to the Nationalist air forces. Ju 86s were again used in the 1939 invasion of Poland, but retired soon after. In January 1940, the Luftwaffe tested the prototype Ju 86P with a longer wingspan, pressurized cabin, Junkers Jumo 207A-1 turbocharged two-stroke, opposed-piston diesel engines and a two-man crew. The Ju 86P could fly at heights of 12,000 m (39,000 ft) and higher on occasion, where it was felt to be safe from enemy fighters. The British Westland Welkin and Soviet Yakovlev Yak-9PD were developed specifically to counter this threat.

At the outbreak of the Second World War, South Africa's Ju 86Zs were militarised and armed as bombers with defensive guns and external bomb racks. The aircraft were initially used for coastal patrols along with the sole Ju 86K-1, playing an important role in the interception of the German blockade runner SS Watussi in December 1939. In May 1940, they were used to re-equip No. 12 Squadron SAAF, which was deployed in the East African Campaign from June 1940. It flew its first bombing missions on 14 June 1940. As more modern aircraft became available, the South African Ju 86s were passed from squadron to squadron, seeing their last use with No. 22 Squadron SAAF, which used it along with the Avro Anson in the coastal reconnaissance role, finally retiring its Ju 86s in September 1942.

Satisfied with the trials of the new Ju 86P prototype, the Luftwaffe ordered that some 40 older-model bombers be converted to Ju 86P-1 high-altitude bombers and Ju 86P-2 photo-reconnaissance aircraft. Those operated successfully for some years over Britain, the Soviet Union and North Africa. In August 1942, a modified Supermarine Spitfire V shot one down over Egypt at an altitude some 14,500 m (49,000 t); when two more were lost, Ju 86Ps were withdrawn from service in 1943.

Junkers developed the Ju 86R for the Luftwaffe, using larger wings and new engines capable of even higher altitudes - up to 16,000 m (52,500 ft) - but production was limited to prototypes.

Sources:
Gunston, Bill - The Encyclodepia of the Worlds Combat aircraft, 1976, Chartwell Books, Inc., New York
Brown, Eric, Captain - Wings of the Luftwaffe, 1979, Airlife Publishing Ltd., Shrewsbury
Gunston, Bill & Wood, Tony - Hitler's Luftwaffe, 1977, Salamander Books Ltd., London
Donald, David - The Complete Encyclopedia Of World Aircraft, 1997, Brown Packaging Books Ltd., London
Wikipedia - Junkers Ju 86