The John W. Allen World War II Collection consists of visual, textual and audiovisual materials documenting Allen's military service as a navigator during the war. Photographic slides documenting the 401st Bomb Squadron's missions from England make up the majority of the collection.

The bulk of the collection consists of 185 35mm color photographic slides taken, for the most part, by Allen during his military service. Twelve slides are informal portraits of Allen during his training in the U.S. The remaining 173 slides primarily depict missions with the 401st Bomb Squadron from Bassingbourn, England over Europe. Images include in-flight shots taken of other aircraft, bombing targets, flak, and aerial views. There are also images of men that Allen served with, including group portraits taken with their B-17, #42-102504 "Time's A-Wastin," as well as images taken from inside the plane of individuals. There are several informal portraits of unidentified servicemen; one image shows Lt. Randall H. Archer holding a Nazi flag. A few slides depict buildings and sites in England. Nose art on the B-17s "Time's A-Wastin," "Qualified Quail" and "Little Patches" is also pictured. A very small number of images depict scenes in the South Pacific from when Allen was serving with the Air Transport Command.

Many of the slides (114) are identified with numerical indexes or notes for slide presentations. However, most of the descriptions are not extensive and images are not dated so cannot be matched to particular missions. Some of the indexes also list slides that are not present in the collection. The 59 slides not identified with indexes are grouped by subject, such as aircraft, aerial views, buildings and people. The majority of slides are originals but some duplicate copies are present. Ten images that were used in the book Serenade to the Big Bird by Bert Stiles were reproduced as 3.5x5-inch prints and also have written descriptions. A roll of black-and-white 35mm film with 26 frames is also present and primarily includes images of soldiers at leisure exploring London. A 5x7-inch color group portrait of the 401st Squadron at a reunion in 2002 is also present.

In addition to the photographic materials, there are three videocassettes documenting the 91st Bomb Group. There is also a typescript draft of an article submitted to World War II Magazine that gives first-hand accounts of the missions of the 401st Squadron. Two small posters produced after the war describe the 91st Bomb Group at Bassingbourn with text and graphics.