Wanderers eased into the second round of the FA Youth Cup to set up a home tie against Hartlepool United or Accrington Stanley.
The Whites ended Wythenshawe Amateurs' impressive run in the competition with goals from Yestin Shakespear, Leo Graham and Wesley Frimpong at the University of Bolton Stadium.
Wythenshawe had battled through four ties to reach the first-round proper but saw their hopes of another upset effectively ended as Wanderers led 2-0 at the break.
Julian Darby’s youngsters weren’t at their fluid best but got the job done in efficient style to continue their impressive start to the season.
And they will now be at home again in round two against Stanley – who knocked them out last season – or Hartlepool, who meet in the North-East on Wednesday night.
Youth team boss Darby said: “The priority is to get through to the next round, and that is what we have done.
“Was it pretty? Did we play very well? No, I think we are much better than that.
“But it is hard against a team who sit back. They do things that the teams we normally play against don’t do, so our lads had to try to counteract this.
“The first goal was always going to be vital and Yestin did well. Then at 2-0, you go into half time breathing a bit more easily and Wes Frimpong scores a great goal to seal the tie.
“It is nice to get into the next round and it is here again, and hopefully we will put on a better show.”
Wanderers, who included six first-year scholars in their starting line-up, went ahead after 20 minutes when Shakespear headed home following a cross by Leo Graham.
Graham added the second himself when he calmly slotted home just before the break.
And Frimpong then wrapped things up with 15 minutes to go when he burst forward from right back and ran onto a through-ball from substitute Danny Jones to finish impressively from a narrowing angle and cap a memorable day for the youngsters who made the most of their taste of the UniBol.
“Ultimately this is what they want,” added Darby. “In a few years’ time, they want to come here and play in front of 25,000 or 30,000 supporters every week.
“It is just what the lads have dreamed of. Joel Burgess and Noah Halford, they are Bolton boys through and through.
“They go watching the first-team games home and away and for them to get to play on here was fantastic. It’s a great experience for everyone.”
Wanderers: Dallimore, Frimpong, Inwood, Halford (Grayson 85), Hogan, Beardsworth, Burgess, Sharples, Shakespear (Jones 68), Fleury (Westwood 79), Graham. Substitutes: Barlow, Lawrence, Lewis, Mancisidor.
Attendance: 472
Images: Finn Watkins