Hughes' men take on a team who have lost just one of 12 Premier League matches at the Etihad Stadium this season, scoring 42 goals in the process.
However, Stoke held the 2011-12 champions to a goalless draw at the Britannia Stadium in September and have since enjoyed top-flight victories over Chelsea and Manchester United.
While Hughes is well aware of the threat his former employers will pose, he believes Stoke can spring a surprise on Saturday.
"We've had really positive results against the top teams this year, beating Chelsea and Manchester United, drawing with City, which very few teams have been able to accomplish, so we were pleased with that performance at the Britannia," he said.
"We'll have to match that and maybe go somewhere a little bit more as well."
City were stifled by Barcelona in the UEFA Champions League on Tuesday, as goals from Lionel Messi and Dani Alves secured a 2-0 away win for Gerardo Martino's side.
However, Hughes feels City will be able to put that disappointment behind them as they turn their attention back to the Premier League.
"They're able to go from one challenge to another and refocus very quickly," he continued.
"They've got a huge squad of great quality. The difficulty from my point of view is knowing who they're going to pick on the day.
"They've been absolutely outstanding at home and averaged a significant amount of goals as well, so it's a huge task."
