The 21-year-old only joined the Potters on a four-year deal this summer after leaving Barcelona, but it had been suggested that he could be loaned out to continue his development.
"We are not thinking about [a loan] at the moment. He's here to learn what the Premier League is all about," Hughes told reporters at a press conference.
"He will play games this year, I'm sure, because he's a good player. I like Marc in terms of his ability. He's getting stronger every day, doing different work here than possibly before.
"He's doing work in the gym that will help sustain his physical level and he's enjoying his day-to-day work."
Muniesa made his debut in Wednesday's 3-1 League Cup win over Walsall.