Many Manhattan Project employees would become Nobel Prize recipients, including Richard Feynman and Luis Alvarez. Albert Einstein, whose warning to FDR was partly responsible for instigating the Manhattan project, had doubts later in life whether this action was proper. A few days before his death in 1955, Einstein signed the Russell-Einstein Manifesto with philosopher Bertrand Russel and nine other famous intellectuals warning about the dangers of nuclear weapons as the Cold War escalated.

Debates about the Manhattan project and the bombing of Japan continue to this day. Opponents point out the massive amounts of civilian deaths and the nuclear arms race that continued for decades into the Cold War.