A typical German sub was built to last four years. Fifty years of turbulent Chicago weather may have proven to be the U-505's most brutal enemy. Indeed, left untreated and outdoors, it would have been unsafe for tours by 2004. And so, in 1997, the Museum launched the largest exhibit conservation project in its history—to preserve the U-505 and move it indoors to a climate-controlled environment.

A large crew spent five months welding, cleaning, repairing and painting the hull. Brackets, stringers and ribs were re-manufactured using original construction drawings recovered from Germany and the patterns from badly eroded parts. It was difficult to find the sub's original color. The Museum conservation team used photos, a German archive painting manual, veteran recollections and more, so the sub could be conserved authentically. Ballast by ballast, tank by tank, the team installed reinforcements, focusing on jacking points and cradle locations. Ultimately, it took more than two years to ensure that the U-505 was structurally sound.