The Berkeley school announced on Wednesday that Martin has resigned from his position "in order to pursue other opportunities".
The resignation comes a day after the Bears' first-round loss in the NIT - an embarrassing upset, as they were a No. 1 seed.
In recent years, Missouri's basketball stock dipped.
He has taken the Golden Bears to the NCAA tournament once in three seasons.
Jeff Goodman first reported Missouri's decision to offer Martin.
Martin has made coaching changes n three-year increments.
Martin coached at Missouri State from 2008-2011, compiling a 61-41 record and delivering the Bears' last regular seasons Missouri Valley Conference Championship in his final season. Martin had to deal with the fallout of an NCAA investigation of Pearl's program, and he got the Vols back to the tournament in his final season.
"We appreciate all that Cuonzo has done with our men's basketball program over the past three seasons, creating excitement inside Haas Pavilion, guiding our team to a pair of postseason appearances and improving the academic performances of student-athletes".
The "Courtship of Cuonzo" may not last long. His.606 win percentage is the highest an incoming coach would bring to Columbia since Mike Anderson (.685 in four seasons at UAB) was hired in 2006.
All the details of his contract have not been released, but the news was first broken by ESPN's Jeff Goodman, who says they are now working on a deal that would land Martin in Missouri for the next seven years.