The left-back made 30 appearances for the Saints across three seasons.
"Last year was a frustrating one for me, so I am ready to get back to my top form and help Colchester push on," he told the club website.
"It's good to be settled now and I've been happy since I first turned up here
"There's a good squad here, the right philosophy in the way to play and a great work rate from all of the lads."
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