The 25-year-old spent last season on loan with The Potters in a deal that was expected to be made permanent.
But the Portuguese side recalled the Dutch international casting major doubts on him ever returning to the Potteries.
But after protracted negotiations, Stoke boss Mark Hughes said he was relieved to secure the player’s return.
Hughes said: “We’ve been close for some time. It’s been frustrating for a lot of people – not just myself.”
Martins Indi proved a big hit last season, making 35 league and cup appearances.
