Andy Carroll gave the visitors the lead at the Britannia Stadium after five minutes but rather than collapse, Stoke rallied and levelled just after the half-hour mark through Peter Odemwingie.
And after further pressure from West Ham, the hosts sealed all three points in the second half as Marko Arnautovic and Odemwingie's second completed a 3-1 win.
"I was really pleased with what we produced, apart from the first few minutes," said Hughes.
"We talked about it (West Ham's threat from set-pieces) so to concede from the first ball in was disappointing, but apart from that I am pleased with what we did.
"We got back on level terms, which was important, then showed real composure when we broke quickly to take the game away from West Ham.
"In the end, we had a number of chances and could have won more comprehensively."
Stephen Ireland was recalled to the Stoke starting line-up in place of the suspended Jonathan Walters and Hughes was impressed with the midfielder's impact.
"I thought he (Ireland) was great," the Welshman added. "I brought him back in to the side and I was pleased to.
"I know every time I bring him in he will give us quality and awareness of when to play the right pass.
"He always gives you goal threat - he had a few (scoring) chances he's probably disappointed with, he could have had two goals himself in the game.
"I am pleased for him, I am pleased for team because it was a big day for us."
