Poulter was tied with Richard Bland and Jamie Spence at 13-under 131. The trio assumed the lead from first-round leader Bernhard Langer, who barely made it through Friday's round due to food poisoning.
Jimmy Rae of Scotland held the bag Thursday and worked through illness as Poulter shot a 65. After the round, doctors ordered him to a hospital, where he was diagnosed with pneumonia and will stay for at least a week.
"Jimmy said all last week he was not feeling well and I told him to take a week off," Poulter said. "But being stubborn, he came over and was sick about 15 times on the course on Thursday.
"It's going to mean a bit of time off for him and a course of antibiotics, but hopefully he'll be back as soon as possible."
For his new caddy, Poulter tabbed Andy Prodger, Colin Montgomerie's caddie who became available when Montgomerie withdrew with a bad back. Prodger made it from his home in Perth, Scotland with just 40 minutes to spare.
"It was difficult for him because I've not had him on the bag before but I gave him a list of how far I hit each club and it worked out well," Poulter said.
Langer was clearly under the weather and unsure whether he would be able to start his round. After beginning with two bogeys, he recovered with a 3-under 69 for 133, one shot behind Ryder Cup teammate Thomas Bjorn (64).
Others the tournament has claimed include Greg Norman, who pulled out Tuesday with a back injury, and Ryder Cup captain Sam Torrance, who withdrew Thursday after nine holes.
Bland shot a 66. He lost in a four-way playoff for the Irish Open in June but earned enough money to secure his 2003 tour card in his first full season on the circuit.
"I took a lot of confidence from the Irish Open and my main aim now is to contend more often so you get used to the situation," he said.
Spence fired a 64, upholding his reputation as somewhat of a low-scoring specialist. He equaled the tour record with a final-round 60 to win the 1992 European Masters after starting the final day 10 shots behind.
"On other courses like Muirfield, par is a good score, but here you have to take your chances because if you aren't you know someone else is," Spence said. "The chances are 13-under might not be leading at the end of the day."
Notable deaths of 2014 [PHOTOS]
UPI horse racing roundup