The 25-year-old former Ipswich Town youngster has made more than 230 appearances for the U's, but was hampered by injury last season.
Contract options have also been taken up for defenders Lewis Kinsella, Kane Vincent-Young and winger Drey Wright.
Wright, 22, has featured 101 times for the U's, while Kinsella, also 22, joined from Aston Villa last summer.
Vincent-Young, 21, featured 23 times last season for the U's.
Colchester United defender Tom Eastman has signed a new two-year contract with the League Two side.