During World War II, Continental's Denver maintenance base converted Boeing B-17 Flying Fortresses, Boeing B-29 Superfortresses and North American P-51 Mustangs for the United States Army Air Forces. 

Denver Municipal Airport in northeast Denver became the site of the Continental-Denver Modification Center for bomber aircraft in July 1942. Continental Airlines operated the facility under the supervision of the Army Air Forces. A Denver Post article explained the Modification Center did not manufacture aircraft but was “devoted to altering, equipping, and fitting new bombers with whatever additional equipment may be needed for any specific flying task at any particular moment.”

In 1943 about eight hundred people worked in three shifts modifying Boeing B- 17 “Flying Fortress” heavy bombers. In April 1943 the Army announced plans to build Modification Center Number 13, a larger facility on ninety acres of land just north of the airport. Costing approximately $5 million, the new hangar and support buildings opened in October and were also operated by Continental Airlines; the Army retained the old center for testing heavy bombers. The new Denver facility was the largest modification center in the country for the B-17 and outfitted a variety of other planes, including the B-29 Superfortress and planes used for photoreconnaissance over Japan. By February 1945, 3,200 people (37 percent women) worked round-the-clock to modify aircraft.

Profits from military transportation and aircraft conversion enabled Continental to contemplate expansion and acquisition of new airliners after the war.