For the second week running Adam Sadler was without several of his key players, with Jordi Hiwula, Alex Henshall, Albert Rusnak and George King all absent from the starting line-up, forcing Sadler to field a less experienced side.
The visitors shone from the start, piling on the pressure and eager to carve out early openings. City did well initially to absorb the advances from Bolton, with goalkeeper Angus Gunn producing a fine save to deny Luke Woodland early on.
But it was the Trotters who took the lead, with Oscar Turelkeld's stunning shot from the edge of the area dipping in over Gunn to give Wanderers the advantage.
Minutes later Bolton made it two when Zach Clough rounded a committed Gunn to slot home and double the visitor's lead.
City looked out-of-sorts and struggled to contain Bolton and their constant advances. Wanderers were only too happy to take advantage of the Blues' hesistancy when in possession.
Further chances for the away side came through Chris Lester, with Gunn forced into making some important saves to keep Bolton's scoring to a minimum. City pressed for a route back into the game but Bolton consistently thwarted the Blues' attack, with Sadler's lads looking short on ideas and confidence.
The home side started the second half the brightest and worked hard to create openings, but Devante Cole's shot was comfortably saved by goalkeeper Lewis Fielding
But Bolton remained resilient in defence and well-organised, coping well with any pressure from City, and gained the initiative again to find a third goal.
With 71 minutes gone, Woodland ran from his own area to fire a looping shot from 20 yards over Gunn into the net. It was no less than the visitors deserved, with a wonderful goal capping a fine display from Bolton.
With City outwitted in possession and Bolton ruthless in attack, the visitors played out the remainer of the game to seal a comfortable and impressive victory at Platt Lane.
