The cartoon opens with images of explosions, gunfire, and heavy artillery; one character even fires into the camera. It is World War I, and the ever-cheerful Bosko is eating down in a trench. Enemy fire destroys his meal, and later a picture of his girlfriend, Honey. Bosko shows a rare moment of anger, but is quickly cheered up by a fellow soldier. The two begin to dance, only to be interrupted by more gunfire. Bosko finally decides to fight back and downs an enemy bomber (actually a pelican) by using a fellow soldier as a cannon. A friendly hippopotamus is shot down by heavy artillery, which Bosko destroys with a pair of longjohns-turned-catapult. He then saves the wounded soldier by unzipping his navel and retrieving the shell inside. The projectile explodes anyway, turning the already black-faced Bosko even blacker and prompting him to exclaim "Mammy!" à la Al Jolson.
"Bosko the Doughboy" is notable for its departure from the standard cartoon formula of its era. Bosko is usually infallibly happy and chipper; "Doughboy" forces him to drop this demeanor and fight back. Other Bosko shorts concentrate primarily on Bosko cavorting with other characters in a musical wonderland; in "Doughboy", Bosko can't dance more than a few seconds before coming under enemy fire. Bosko's cartoons generally have little to no conflict; "Doughboy" is nothing but fighting. In short, "Bosko the Doughboy" is almost a total departure from other shorts in the series (and from those of other studios of the time). It is usually regarded as a high point of the character's cartoon career.