The right-back has spent the last 18 months at the Mazuma stadium, on two separate loan deals from Burnley, and has made 57 appearances for the club to-date.
Manager Stephen Robinson believes Cooney’s presence will prove to be an important part of the squad.
“Ryan's a young boy, he did well last year,” he said.
“We've secured him on a two-year contract, not a loan deal this time so we create an asset straight away.”
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The Manchester-born defender has played 4,362 minutes so far for the Shrimps, scoring two goals and providing two assists as well as delivering 79 crosses and regaining possession 45 times in the opposition half.
Robinson added: “I think there's a lot more to come from Ryan, he's a young boy still learning the game and I think in certain games he's been excellent.
“Ryan has a big future ahead of him if he continues to do the right things, which we believe he will.”