The Welsh midfielder inspired a much-changed, but still strong, Stoke team to a 4-0 victory over the League One side at the bet365 Stadium on Wednesday night.
Allen scored twice and set up Peter Crouch before he was substituted at half-time after complaining of a minor back niggle. Ramadan Sobhi completed the scoring after 80 minutes with his first goal for the club.
Allen's former club Swansea recently enquired about the chances of taking the 27-year-old back to the Liberty Stadium, but Potters boss Mark Hughes has always seen him as a figure to help fill the void left by the departure of experienced players such as Jonathan Walters and Glenn Whelan over the summer.
"I thought Joe was excellent. He was an obvious choice (as captain) and he will step up and fill the gap in terms of leadership and direction of the group," said Hughes.
"There was never any danger of us allowing him to leave. He clearly has a connection with his previous club and there was an interest, but we said no.
"He came off but he's fine. He was a little bit stiff in his back and we didn't want to take any chances, so we took him off and had the experience of Darren Fletcher to bring on."
Hughes made eight changes from the side that started the Premier League win against Arsenal at the weekend, handing a debut to summer signing Josh Tymon.
The 18-year-old, bought from Hull, impressed down the left-hand side and almost scored a deserved goal, but saw his second-half effort strike the crossbar.
"We wanted to see Josh in that position (left-wing back)," said Hughes. "He's come with a view to give competition to a number of players on that left-hand side and could have scored, he deserved a goal with the quality of his performance.
"He's still got things to learn, but for his first performance at senior level he did really, really well."