Ivan Toney’s first-half header proved decisive for Posh, who kept up the chase on Ipswich and Wycombe in the automatic promotion places.
Bolton played a back five for the first time this season and though they rode their luck in the first 45 minutes, another shift in formation saw them ask serious questions of their hosts after the break.
“We changed the shape, the system and they changed theirs – they had used 4-1-2-1-2 at home,” said the assistant boss. “First half, the cross coming in, we had to do better. It was almost a free header and you can’t let players of Peterborough’s quality have that sort of time in the box.
“Second half there was a real response. We went at them, downhill, with the wind, and caused them more problems. We just didn’t finish them off in those moments.
Wanderers’ most clear-cut opportunity fell to Luke Murphy who steered a free header wide from Josh Emmanuel’s right-wing cross.
“It was a great chance,” Flitcroft said. “He sprung the midfield trap, his timing was good and the quality of the ball is excellent. He almost had too much time to hit the target.
“The boys gave us everything they physically had, so that’s all we can ask for away from home.”
Wanderers had struggled to make much of an attacking dent on Peterborough in the first half – and Darren Ferguson’s side could have had a greater lead with good chances falling to Mark Beevers and Mo Eisa – who hit the bar and had another effort blocked on the line by Josh Earl.
They had a greater share of the game in the second 45 minutes but Flitcroft believes it would have been foolhardy to gamble more bodies forward in attack from the first whistle.
“You are coming to Peterborough, one of the highest scoring sides in the land, so you have to give them some respect. You have to make sure you limit them to chances,” he said.
“You saw they put one quality ball into the box in the first half and we just weren’t set for it. Toney got a free header. We have to make sure we are more solid than that.
“You don’t go 4-4-2 against Peterborough first half. We took them by surprise second half and forced the issue. Darren (Ferguson) was screaming for his players to get the ball down and play through but they couldn’t, we suffocated them.
“Luke’s chance was probably the one we’d been waiting for. They could have been further ahead with the chances they created first half, or that we created for them. When your opponents have that sort of firepower on the pitch, sometimes you have to ride your luck and wait for an opportunity.”
Wanderers remain 15 points from safety but Flitcroft reckons the new system could bring a better chance of points away from home.
“Every day we are demanding more from them,” he said. “We keep trying to drive forward.
“We have to try and move this away record into positive points. We have to find a formula.
“We tried a different system to give the players something different to focus on and it’s something that we will examine the detail and keep doing it until we get it right.”