Two goals in the second half for the Wanderers forced defeat upon Simon Weaver's men despite a positive showing.
The visitors had started the game strongly at took the lead inside 15 minutes thanks to an own goal and they went into the break with a deserving lead but goals from Lloyd Isgrove in the 53rd minute and Eoin Doyle in the 78th minute secured Bolton the three points.
There we no changes to Town’s starting XI but different faces were on the bench as Aaron Martin missed out with an ankle injury.
It meant veteran striker Jon Stead was brought into the squad, along with Joe Cracknell who was part of the 17-man squad for the first time this year.
A two-minute silence was held before kick-off as both teams paid tribute to the life of HRH The Prince Philip, Duke of Edinburgh.
It was Weaver’s men who started on the front foot and could have been ahead inside the opening four minutes as Thomson dragged an effort just wide from the edge of the Bolton area.
It was a really promising start from Town and they got their rewards on the 13th minute when a Bolton own goal opened the scoring.
All the hard work had been done by Muldoon and Thomson. The former crossed from the right and the latter forced a save from Gilks but the keeper could only parry to his own defender Gethin Jones and the ball bounced off him into the net to give Town a deserved lead.
Town then stayed in the ascendency approaching the half hour mark as McPake saw an effort blocked after Kerry had done ever so well to steal possession in the Wanderers half.
Then out of nowhere, the home side had a great chance to equalise when Eoin Doyle latched onto a simple ball over the top and it seemed it would be a simple finish into the bottom corner for the prolific striker, but James Belshaw had other ideas and pulled out a really important save low to his left to keep his side’s lead intact.
Doyle would get another chance ten minutes later as he found himself unmarked at the back post. The striker brought the ball down and looked to poke it into the far corner but he got the effort all wrong and the danger was no more.
Town ended the half with a yellow card shown to Lloyd Kerry for a late challenge on Marcus Maddison.
The first bit of action in the second half was in fact the second goal of the afternoon but it came for Bolton who now looked a more threatening outfit.
Lloyd Isgrove picked up the ball on the left side and took aim just outside the Town area. The shot went through bodies and caught Belshaw unsighted and he couldn’t react quickly enough to stop the ball nestling into the far corner on the 53rd minute.
Neither side were creating too many clear-cut chances following the equaliser and the game looked to be heading for a draw before a mistake at back for Town cost them dearly.
The ever-solid Connor Hall miscued a back pass to Belshaw in the 78th minute and it allowed a run at goal for Doyle. The striker who has been in great form this season picked his spot and smashed the ball past Belshaw to complete the turn around.
Town reacted well with Stead forcing a great save from Matt Gilks in the Bolton goal but Weaver’s failed to find the equaliser.
The next chance to get back to winning ways is on Tuesday as we take on Leyton Orient at the EnviroVent Stadium.
Bolton Wanderers: Gilks, Jones, Williams, Almeida Santos, Doyle, Maddison (Thomason 46), Isgrove (Elbouzedi 76), Baptiste, John, Lee, Afolayan (Delfouenso 74).
Subs not used: Tutte, Miller, Brockbank, Gnahoua
Goals: Isgrove 53’, Doyle 78’
Town: Belshaw, Jones, Falkingham, Smith, Burrell (Fallowfield 83), Thomson, Beck (Stead 62), Kerry (Francis 67), Muldoon, Hall, McPake (Kiernan 67)
Subs not used: Cracknell, Williams.
Goals: G. Jones (OG) 13’
Cards: Kerry, Francis
Referee: Sam Allison