Marshall scored twice in 17 appearances for the League Two side and Cobblers boss Ian Sampson feels the 18-year-old will have benefited from his first taste of senior football.
"Stoke want Ben to go back to them and so he will return," Sampson said. "We are really grateful to Tony Pulis and Stoke for allowing us to borrow Ben."
He added: "When he came to us on loan he had only just joined Stoke and I think the three months here will have done him good. Now Stoke want to have a closer look at him."