The 42-year-old rejoined the Coca-Cola League One side last summer and was expected to mount a promotion challenge but a run of poor form has seen the Dons lose touch with the play-off places.
Friday morning's papers reported that former England captain Ince was set to be sacked as part of a cost-cutting campaign at stadium:mk but he has now decided to resign.
However he will stay on for the last four games of the season before leaving next month.
Source: PA
Source: PA