The Republic of Ireland international, 29 has joined the Sky Blues on a free transfer after chalking up more than 200 appearances for the Iron.
His contract ran out in the summer and he was not offered an extension after making it clear he wanted to stay in the Championship
He began his career at Tranmere and has also had spells with West Brom and Sunderland, from whom he joined the Iron from in 2006.
Sky Blues boss Andy Thorn said: "Joe is proven quality. He's an international and I've liked him for a long, long time. We tried to get him at the same time that we brought Keiren (Westwood) to the club so we are delighted to have him on board now.
"It's been a terrific day for the club to get two very good goalkeepers in and I think this gives us a really good backbone to build on."