Jeter and the MLB club announced the news on Monday, citing differences between the two.
“Today I am announcing that the Miami Marlins and I are officially ending our relationship and I will no longer serve as CEO nor shareholder in the club,” said Jeter in a statement.
“We had a vision five years ago to turn the Marlins franchise around, and as CEO, I have been proud to put my name and reputation on the line to make our plan a reality.”
Jeter added: “That said, the vision for the future of the franchise is different than the one I signed up to lead. Now is the right time for me to step aside as a new season begins.”
He thanked the staff, Marlins fans, players and the Miami community for welcoming he and his family “with open arms”.
Marlins chairman and principal owner, Bruce Sherman, thanked Jeter for his contributions, but is looking to the future.
“We have a deep bench of talent that will oversee both business and baseball decision while we work to identify a new CEO to lead our franchise,” he said.
“The ownership group is committed to keep investing in the future of the franchise – and we are determined to build a team that will return to the postseason and excite Marlins fans and the local community.
Sherman wished Jeter luck in his future endeavours.