Paul Sheerin's young guns faced their toughest assignment of the season so far when they travelled to Fife to face League One Raith Rovers whose confidence would have been lifted by their 2-0 victory at home to Stenhousemuir at the weekend.
Miko Virtanen lined up at right back, where he had played for Finland in the Euro Under 19 championships, while Ryan Harrington slotted in at centre back alongside Sam Roscoe. Raith boss Barry Smith brought Lewis Milne and Iain Davidson into his starting eleven.
Both sides saw plenty of the ball in the early stages as they sized each other up. A dangerous run from Connor McLennan saw him fizz the ball across the edge of the six-yard box, but there was no-one in a red shirt who could take advantage.
Ethan Ross was crowded out before he could get a shot away after good work from Bruce Anderson as the Pittodrie youngsters put some pressure on the Rovers defence. The home side almost created an opening on 11 minutes, but Flanagan was beaten to the ball by some alert goal-keeping from Archie Mair.
A dangerous ball in from the left from Flanagan saw the ball diverted behind for a corner by Ryan Harrington but the flag-kick came to nothing. However, Rovers were not to be denied and in 16 minutes they took the lead in spectacular fashion when Nat Wedderburn fired a left-footed shot high into the net leaving Mair helpless.
Good work from Morgan Brown and Anderson created a shooting chance for McLennan but the Rovers defence blocked his powerful left-footed effort. Moments later Anderson was denied by a fine tackle on the edge of his own area by McKay as the Dons pressed for an equaliser.
A superb ball from Brown almost got Anderson in, but his twenty-yard effort lacked the power required to test Raith keeper Wright. It was encouraging to see the response from the boys to going behind.
The League One team doubled their advantage in the 28th minute when Ross Matthews drove the ball home from the edge of the area. Aberdeen pleas for a foul in the build-up on Sam Roscoe fell on deaf ears.
Two minutes later it was 3-0. Again, it looked like there was a clear foul on Dean Campbell by Wedderburn as he won the ball for Nisbet to run through and score. Referee Grant Irvine wasn't endearing himself to the Dons backroom staff.
In spite of the scoreline, the Dons youngsters were battling hard, but the confidence was starting to flow through Rovers veins and they were playing some nice football.
The half-time whistle blew with the home side in the ascendancy although it was a rather harsh scoreline on Aberdeen but luck, and the referee, didn't appear to be on their side.
Half time Raith Rovers 3 Aberdeen Colts 0
Aberdeen made a change at the interval introducing Lloyd Robertson in place of Ethan Ross. Lloyd slotted in to centre-back as Harrington moved to right back and Virtanen went into midfield.
The home side dominated the territorial possession in the opening minutes of the second period but another fine cross from McLennan created the nearest thing to a chance but, again, there was no Dons man to convert the opportunity.
Big Connor was in the thick of the action again on 56 minutes, cutting in from the right to force Wright into a good diving save. We were maybe three down, but we weren't going to go out of the competition meekly.
On the hour, Barry Smith made a double switch taking off Gillespie and Nisbet while bringing on Valentine and Duggan.
Aberdeen were proving to be far more resilient in the second half but were finding the Kirkcaldy back division tough to break down as they battled to get back into the game.
An angled drive from Milne flew over as Rovers chased a fourth goal with the game going into its final quarter. Archie Mair then saved well from Flanagan before Matthews blasted the rebound high over.
The home side made their final change on 71 minutes as Buchanan replaced the sprightly Flanagan.
Bruce Anderson reduced the deficit with a stunning goal on 72 minutes. The striker picked up a neat through ball from Brown before unleashing a terrific right-footed effort which fairly flew into the keeper?s top right corner. A fantastic finish from a young man with a huge future.
Sean Linden was introduced on 75 minutes, coming on for a tiring McLennan. A deep corner from the left by Campbell picked out Roscoe beyond the far post but he couldn't quite direct his header on target.
Jack MacKenzie was booked in the 80th minute for a strong challenge on Wedderburn. Moments later the young full back tried his luck from long range, but Wright saved comfortably.
Duggan wriggled clear of the Dons defence on 85 minutes but lost his composure as he shot wildly high and wide. As the game went into its final minutes, Chris Antoniazzi came on for Brown and almost had an immediate impact forcing a good save from Wright who couldn't hold on to the ball. Unfortunately, neither David Dangana nor Dean Campbell was able to convert the rebound after the keeper's spill. Had it gone in, we would have had a grandstand finish.
Aberdeen were finishing strongly but time ran out on them and so Raith Rovers go through with our best wishes. A much improved second half showing from the Pittodrie youngsters but ultimately to no avail.