Ibehre returns to the Weston Homes Community Stadium on a permanent basis having spent the first half of this season on loan with the U's.
The 29-year-old joined the Dons from Walsall on a free transfer in the summer of 2009 and went on to make 112 appearances for the Milton Keynes club, scoring 15 goals.
He told mkdons.com: "I have had an incredible time at MK Dons. I've really enjoyed every minute of it and I have learned a lot along the way. I have made some great friends and it is a club I will always hold close to my heart.
"I have had some great moments with the club and the fans have always offered me incredible support through thick and thin. They have always stood by me, shown great faith in me and I am extremely thankful to them.
"I would like to wish everyone at the club the best success for the remainder of the season.
"My aim now is to open a new chapter in the book with Colchester. I had a great time on loan there and I am excited about playing games. We have a challenge on our hands at the moment, but the team feel confident."
Colchester are currently in the npower League One relegation zone, two points adrift of safety.