For much of its career in Australia, the fuselage of the Southern Cross was painted dark blue, often described as Royal Blue. When the aircraft was restored for display in 1958, although attempts were made to retrospectively replicate the configuration of the 1928 Pacific flight, the fuselage was again painted dark blue. However, when the aircraft flew the Pacific, the fuselage was painted a lighter shade of blue.

Available photographs suggest that when Sir Hubert Wilkins operated the aeroplane as the Detroiter it was painted a dark shade of blue. When Smithy acquired the future Southern Cross from Wilkins, the aircraft was located in Seattle so it is hardly surprising that Boeing were contracted to restore the aeroplane to airworthiness. Boeing's involvement is described by author Peter M. Bowers⁽²⁾.

Boeing's scope of works is unknown but it did include fitting three new Wright J-5-A Whirlwind engines (serial numbers 7416, 7417 and 7418) and Westinghouse Micarta propellers as well as additional fuel tanks for the proposed Pacific flight. The aircraft was originally powered by J-4 Whirlwinds and reportedly the later model engines were diverted from a USN order involving some behind the scenes string-pulling. Clearly Boeing also completed other work to make the aeroplane airworthy because it was subsequently flown from Seattle to Mills Field, San Francisco.

John Stannage⁽³⁾ stated that when the aeroplane emerged from the Boeing factory it had "deep-blue fuselage and silver wings". Photos of the aircraft soon after arrival at Mills Field suggest that the fuselage was a dark shade but as will be seen later, the wings were not yet silver.

In preparation for an attempt on the world endurance record, the aircraft went to Douglas at Santa Monica for further modifications which included:

There ensued a series of attempts on the endurance record but all were unsuccessful.

After Capt Allan Hancock offered to sponsor the Pacific flight, the aircraft went back to Douglas, its third visit, for the following work:

* Smithy⁽⁴⁾ states; “A new fabric cover for the fuselage was needed ...”

Obviously, recovering the fuselage would also require painting and indeed when the aeroplane emerged from the Douglas factory, its fuselage was painted a lighter shade of blue.

An article on the Southern Cross in Air Pictorial of April 1966 prompted a subsequent response from K.M. Molson, Curator of the National Aviation Museum of Canada:

This being the case, there can be little doubt that the colour used was what was popularly known as "Trainer Blue", a shade that was then in use by the U.S. Army. This colour is defined on this 1922 U.S. Army specification as "Light Blue No. 23". This colour underwent some slight changes over the years, finally being renamed "True Blue" in the mid-1930s.