The 21-year-old was one of Hughes' first signings as Stoke manager when he completed his free transfer from the La Liga champions, signing a four-year contract at the Britannia Stadium.
With fellow defender Erik Pieters also arriving, Muniesa faces a battle to break into the Premier League outfit's first team.
But the Spaniard impressed his new manager in his first appearance for the club in their 3-1 League Cup victory over Walsall in midweek, and Hughes has no intention of loaning him out.
"We are not thinking about that (a loan) at the moment," Hughes said. "He's here to learn what the Premier League is all about.
"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."
