The 29-year-old, who joined Aberdeen last summer after leaving Dundee United, previously had two years left with the Dons, but is now tied to the club until the summer of 2017.
The Irishman is happy to have committed himself to Aberdeen and has praised the impact of manager Derek McInnes at Pittodrie.
“I had two years left so wasn’t even thinking about a new contract but the gaffer took me aside and said he wanted me to sign the same length of deal as him,” said Flood in the Daily Record.
“We have a lot of respect for each other and he has brought the club a long way in a short time. Aberdeen can go even further with him in charge and I want to be part of that.
“There are a lot of boys on the same length of contract now so he is planning for long-term success.”
McInnes added on the club's official website: "Since his arrival, Willo has been a consistent and positive influence on our team and to our club as a whole.
"He has been an integral player for us, playing such an important part in our recent successes, and he will continue to be so going forward."