But as he is under 24, the Potters are entitled to a transfer fee as compensation for their development of the player.
And with the two clubs unable to settle on a price, a tribunal at the end of September will dictate how much the Iron must pay.
"We will emphasise the cost of developing a youngster like Martin, who progressed right through our Academy from a very early age," said Stoke director of football John Rudge, speaking to the Stoke Sentinel.
"His form (at Scunthorpe) just goes to show the promise Martin has. He's young, hard-working, very enthusiastic and has a bit of pace. We were confident he would have figured in our squad this coming season."