U.S. District Judge William H. Pauley granted the release of a redacted warrant against the will of prosecutors Tuesday after five news organizations requested the documents, citing high public interest.
The FBI probe into Cohen's emails started in July 2017, less than six months after Trump took office.
The documents came from Cohen's office, apartment, hotel room and a safe deposit box. Some were recovered from a shredder while others were culled from cellphones, iPads and computers.
Lanny Davis, a lawyer for Cohen, said Monday that the documents furthered his client's "interest in continuing to cooperate and providing information and the truth about Donald Trump and the Trump organization."
Last month, Cohen told a congressional committee that he believes Trump is a racist, a con man and a cheat."
The documents reveal illegal payments from Trump's campaign to silence women who claimed to have had affairs with him.
Pauley said that some documents had to be redacted because they would jeopardize ongoing investigations. Information related to a campaign finance contribution scheme is entirely redacted in the documents.
Prosecutors with special counsel Robert Mueller first obtained search warrants for three of Michael Cohen's email accounts starting in the summer of 2017 before the case was referred to U.S. District Court for the Southern District of New York.
The FBI took more than 4 million electronic and paper files from Cohen's Manhattan home during the raid.