The Giants said Manning -- who spent all 16 seasons of his NFL career with the Giants after a draft-day trade in 2004 -- will formally announce his retirement on Wednesday.
"For 16 seasons, Eli Manning defined what it is to be a New York Giant both on and off the field," said John Mara, the Giants' president and chief executive officer. "Eli is our only two-time Super Bowl MVP and one of the very best players in our franchise's history.
"He represented our franchise as a consummate professional with dignity and accountability. It meant something to Eli to be the Giants quarterback, and it meant even more to us."
Manning, 39, led the Giants to Super Bowl victories over the New England Patriots after the 2007 and 2011 seasons.
He is one of just five players in NFL history with at least two Super Bowl MVPs, a club that also includes Joe Montana, Bart Starr, Tom Brady and Terry Bradshaw.
But he spent most of 2019 as backup to rookie quarterback Daniel Jones, starting just four games. Set to become a free agent, Manning had made it clear he didn't relish the backup role.
Manning, younger brother of another superstar quarterback, Peyton Manning, started 234 games for the Giants -- the fourth most by a quarterback for one club.
He was drafted first overall by the San Diego Chargers in the 2004 draft but he made it known he didn't want to play in San Diego and was traded to the Giants.
- 'A privilege to coach' -
He finishes his career seventh all-time with 366 touchdown passes, seventh in passing yards with 57,023, and tied with Joe Montana for 11th in career wins with 117.
But he'll be best remembered for two of the biggest upsets in Super Bowl history.
In February of 2008 the Giants stared down Tom Brady and the New England Patriots, ending New England's bid for a perfect season.
Manning's MVP performance included a miraculous completion to David Tyree, Manning escaping the grip of Pats defenders to find Tyree, who held the ball against his helmet long enough to make the pass complete.
Manning then found Plaxico Burress with the game-winning pass with 35 seconds to play.
Manning and the Giants beat the Patriots again to cap the 2011 season.
"It was an honor and privilege to coach Eli, and to go through the wonderful and magnificent moments that he and his teammates provided for all of us in the world championship '07-'08 and '11-'12 seasons," former Giants coach Tom Coughlin said.
"He's an incredible big-game performer. You talk about a guy that's great to coach, focused every day, took tremendous pride in preparing, practice, had a great sense of humor, was a cynic in the locker room. But the guys loved him, and they loved him for it, and they played for him."