It was a disappointing evening for Rovers at the Reebok as the Under-21s went down to a 3-0 defeat.
Zach Clough grabbed a goal in each half, either side of a Conor Wilkinson strike as Rovers struggled to cope with the hosts.
Dean Rittenberg rattled the woodwork for Rovers, but it was a rare chance as Bolton had the better of the game once they scored their opening goal.
They could have added further to their tally in the closing stages but they'll be more than happy to clinch a first win of the season.
Despite the result it was Eric Kinder's side that started the brighter of the two under the Reebok lights.
Rovers welcomed back Darragh Lenihan and John O'Sullivan after injury and the two combined to create the first clear opening on 13 minutes.
O'Sullivan found Lenihan with a ball down the right and as he cut inside Lynch did well to save the shot.
Despite that bright start it was the hosts who took the lead a minute later.
A slick passing move through the centre saw Rovers carved open and Zach Clough had time and space to finish cooly past David Raya.
Rovers had a great chance to respond immediately after Dean Rittenberg had been brought down just outside the Bolton box, but John O'Sullivan was a whisker away with the free-kick going narrowly over the angle.
Rovers continued to force the pace but it wasn't until the 37th minute that Lynch was called into action once more. Rittenberg with a fierce shot to the near post that the Bolton 'keeper had to beat away.
The Trotters then had two great chances to double their advantage. The first on 39 minutes when Clough fed Chris Lester through on goal, but he inexplicably wanted more time and his eventual shot was blocked.
A minute later and a defensive mix-up almost presented Bolton with a second, David Raya saving well to deny Conor Wilkinson.
Any chance of an equaliser at the start of the second half evaporated just five minutes after the restart.
With Rovers on the attack a mis-placed pass from Rittenberg saw Bolton break quickly, Chris Lester showing great pace down the flank to centre from the right to where Conor Wilkinson converted from close-range with an outstretched boot.
The home side then had two lucky escapes, firstly as Rittenberg stayed on his feet in the area under the challenge of the already booked Hayden White before the Academy striker fired against the crossbar from an acute angle.
A third almost arrived just before the hour mark when Tom Youngs robbed half-time sub Will Beesley, but his near-post shot was saved well by Raya, it would arrive soon after however as Youngs strong run was finished off by Clough for his second of the game.
As the half wore on it was Bolton who continued to pressure, Youngs, now playing further forward, spurned three great chances to stretch their lead further.
At the other end Will Beesley almost reduced arrears after cutting inside to shoot left-footed but Bolton 'keeper Lynch saved well.
Wanderers ended the game with further chances, David Raya saving a Jan Gregus free-kick, whilst sub Aaron Knight headed wide with the goal at his mercy.
The only pleasing aspect on an otherwise disappointing evening was the return to action of John O'Sullivan and Darragh Lenihan. O'Sullivan getting just over an hour under his belt whilst Lenihan will be all the better for his first 45 of the season.
BOLTON: Lynch, White, Kellett, Threlkeld, Bolger (c), Kelly, Lester, Gregus, Wilkinson (sub Knight 80 mins), Clough (sub Ariyibi 64 mins), Youngs.
Subs not used: Campbell (GK), Holding, Matthews.
Goals: Clough 14, 63 mins, Wilkinson 50 mins.
ROVERS: Raya, Lenihan (sub Beesley 46 mins), Bauress, Paulo Jorge (sub Edinho 66 mins), O'Connor (c), Tumwa, Fernandez, O'Sullivan (sub Daly 62 mins), Rittenberg, Green, R. Hanley.
Subs not used: Urwin (GK), Paul.