An interesting theory from Marvel Studios explains why the super soldier serum deformed Red Skull but not Captain America.
Red Skull is the true nemesis of Steve Rogers, since the leader of HYDRA It's a twisted reflection of the Captain America. Both characters of the Marvel Cinematic Universe they took the super soldier serum from the Dr. Erskine, but while the latter became a model of strength and courage, the former was horribly deformed, hence the nickname given to it by Adolf Hitler. But why exactly did this happen to the villain?
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Dr. Erskine tells Steve that it is because the serum amplifies the properties that are already within the person taking it ("good becomes great, bad becomes … worse"). However, this does not really explain the physical transformation that Schmidt went through. But luckily there is a theory that solves it in a better way.
The penicillin injection that Erskine gives Rogers before his treatment was the most important part of the process that Schmidt overlooked.
In the scene of the transformation of the slim Steve Rogers into the great Captain America there is a little joke in which Erskine injects him with penicillin beforehand. The penicillin injection was much more important than it sounds, because the human body is full of bacteria and the Super Serum would also improve microbes. Therefore, they should be killed beforehand.
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It is possible, then, that the bacteria in Schmidt amplified, causing them to eat his face and, presumably, his body.
In the movie, Johann Schmidt is shown injecting the serum himself. It worked, but it left very important physical consequences that caused terror even to his collaborators. And it would have killed him if it hadn't been improved as well. So his body is in a constant battle against super microbes and that ruined his face. This process turned him into the Red Skull.
Despite his terrible disfigurement, Red Skull has lived an incredibly long life. Tesseract (Space Gem) was thought to have killed him in 1945. But in fact, he remained a prisoner on Vormir, tasked with protecting the Soul Gem for decades.
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