Police were responding to a call about an attempted burglary when they pulled over a car matching the alleged suspects' vehicle.
Inside the car, officers found two men with their faces blackened with permanent marker.
Police said the caller described two men with painted faces attempting to break into an apartment Friday night before driving off.
Matthew McNelly, 23, and Joey Miller, 20, were arrested at gunpoint after officers were told they might be armed. Neither man had a weapon. McNelly and Miller were each charged with attempted second-degree burglary.
Both men were released after posting bond.
US blogs, including the popular Huffington Post, described the face markings as "the worst disguise ever".
The men may have been under the influence of alcohol when they devised the idea for their disguises, police chief Jeff Cayler told Radio Iowa
"For what it's worth, it appeared they had both been drinking quite a bit and maybe weren't thinking quite rationally," Mr Cayler said.
"It's a little weird. I've been here long enough that I've seen a lot of things, but this one's a little different compared to most ... I mean, just the face thing is what sets it apart."
