The French midfielder, who joined the club last year, has played in every minute of the Potters' Premier League games so far.
Hughes has revealed that he underestimated the talent of N'Zonzi when he first took over the job at the Britannia Stadium and believes that his side's style will help him improve even further.
"Until you work with players on a daily basis you can underestimate their talent," Hughes told reporters.
"I was one who maybe didn't put Steven into the bracket of a top Premier League player.
"He still has faults that he has to work on, he understands that, but the way we play will bring the best out of him."
Stoke paid £3m to sign N'Zonzi from Blackburn Rovers.