Goals from Mohamad Salah, Frank Lampard and Willian consigned the Potters to a heavy defeat in the capital, and Hughes says that his key players did not perform to their usual standard.
"We weren't good enough today truth be told," he told Stoke City Player following the encounter.
"We came up against a very good team and when that happens you need every player to play at their maximum, and unfortunately today a number of players didn't perform to the levels they are capable of.
"As a consequence of that, it is very difficult to come to a place like Stamford Bridge and influence the game in the manner that you would like. We needed a real high-energy game here today and unfortunately for us we just weren't able to produce that."
The Blues moved top of the Premier League table as a result of the win, while Stoke remain 10th.