The 21-year-old defender, who joined the Potters from Barcelona in July, made his Premier League debut in a 4-0 defeat at Goodison Park after regular starter Robert Huth had been forced to undergo minor knee surgery.
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"We will have to look at the options we have got and then make a decision," Hughes told The Sentinel.
"He [Muniesa] did okay on a difficult afternoon and will be better for the experience. He wasn't the reason we lost. Out of the back four, he was one of the better performers.
"At some point we are going to have to learn about these players, and I feel Marc has been really patient. I couldn't keep disappointing him. I felt it was an opportunity to test him at this level."
Hughes was able to provide an update on Huth, who limped out of the previous weekend's win over Sunderland, and expects him to return to action in a month.
"We were worried they [the surgeons who performed Huth's operation] might find something major, but apparently it was straightforward and the best-case scenario in terms of what was found," added the Stoke boss.
"The surgeons were happy with it. They trimmed the meniscus to stop it flapping about. He'll be out for three to four weeks."