Eleven days on from beating the Blues on penalties at the Britannia Stadium in the Capital One Cup, Hughes' side added to the London outfit's woes on Saturday with a 1-0 triumph over them at the same ground in the Barclays Premier League.
Marko Arnautovic volleyed home in the 53rd minute to condemn Chelsea - whose manager Jose Mourinho was absent from the ground due to his one-match stadium ban - to a third league defeat in a row, and seventh of the campaign.
And Hughes said after the game: "(That was a) good day in the office.
"We played really well and knew we would have to
Obviously at the moment they are not getting positive results but we had to work exceptionally hard against them in the cup and we knew we'd have to again.
"We did, and as a consequence we got the three points, which was massive for us.
"You know at some point they will ask questions of you - they have fantastic individual talent within a great team.
"So you have to stick at it, and we have been able to go up the other end and score a great goal ourselves.
"We showed great qualities once again and there were big performances by everybody - I am delighted."
Chelsea had plenty of possession over the course of the contest and went close to levelling when Pedro struck the post.
There was also a scare for Stoke late on when Blues substitute Loic Remy hurdled a challenge from goalkeeper Jack Butland and stumbled as he tried to shoot, with the effort missing the target and referee Anthony Taylor awarding no penalty.
Hughes - whose side are up to 12th in the table - said of that incident: "Credit to Remy at the end.
"He could have looked for a penalty and time and time again you see Premier League players flailing legs behind them just to get contact.
"He didn't do that - he hurdled Jack and credit to him, he was looking to score a goal, as all strikers should.
"He could have been a little bit more cynical and looked for the penalty, and who knows - at that stage it probably would have been given."
Hughes admitted it had been strange not to have his opposite number Mourinho alongside him on the touchline and felt sure Chelsea would have missed the presence of their manager.
"I haven't experienced it before where the opposition manager is not standing in the technical area next to me," Hughes said.
"In terms of the influence you can have on your team, most of the work is done beforehand.
"But obviously half-time is a key time of the match and sometimes you can affect things in the correct manner.
"It is dependant on the manager
And with a manager the quality of Jose, I would suggest yes, they would have missed him to be perfectly honest - to give him credit for his standing in the game."
Source : PA
Source: PA