Wanderers’ under-18 side were narrowly beaten at home to Manchester United in their first game in the Barclays Under-18 Premier League Elite Group.
Striker Zach Clough grabbed both goals for Bolton but goals from United’s Jack Barmby, James Weir and James Wilson's injury-time winner ensured the visitors went away with three points.
The match at Lostock was their first since the Christmas break and the Whites started the game brightly, creating a couple of good chances through Tom Youngs.
A breakthrough came in the 20th minute when Youngs was involved once again, providing a brilliant pass for Clough who netted from eight yards.
United fought hard to get back in the match and their work paid off just before half-time when Barmby, an England Under-19 international, fired into the top corner from outside the box.
The second half started off slowly with neither side creating many chances until Youngs thought he had made it 2-1, only for the goal to be ruled out by the assistant referee for a push.
It was the Reds who went 2-1 up after 70 minutes when Louis Rowley’s cross was volleyed in by Weir.
With minutes to go, Wanderers thought they had salvaged a point when Clough bagged his second of the game firing in a terrific free-kick.
However, Wilson snatched all three points for United in the 91st minute.
Under-18s' head coach David Lee said: “Overall, we need to learn how to see the game out after working hard to equalise, showing inexperience to concede a goal in injury time.
“This was the first game the players had played together since before the Christmas break so we need to work harder now to recapture individual and team form.”
Wanderers play Reading at the Madejski Stadium in the FA Youth Cup third round on Wednesday 16 before a league game away to Chelsea on Saturday.
Wanderers: Sievers, Gibson, Bailey (Hamer, 85), Holding, Maher, Woodland, Newby, Wolstenholme (Hendrie, 55), Clough, Youngs, Walker