They took an early lead against MK Dons with Daniel Hutchins (pictured right) credited with the goal after a scramble from a corner.
MK Dons made it 1-1 from the penalty spot but we soon led again when David Hutton converted from Tomas Pekhart's cross.
MK Dons levelled again before half-time, we then missed a penalty and the visitors then rattled in four goals in the final half-hour.
It was only the lads fifth defeat in 28 league games this term and they will nevertheless finish third in their group.
Coach Alex takes up the story. "We went 1-0 up very early on after a scramble, conceded a penalty for 1-1 but then David Hutton made it 2-1 from Tomas Pekhart's cross.
"MK Dons equalised before the end of the first half and we were then awarded a penalty for handball but Tomas missed from the spot.
"It then went a bit crazy. We conceded on the hour for 3-2 and then a combination of defensive mistakes, a couple of goals from 30 yards and then trying to get back into it meant MK Dons were able to score a couple more.
"It was a disappointing way to end such a consistent season in the league.
"We let ourselves down on the day but I'm sure this result won't take the gloss off what has been such a positive season."
Under-18s: Stroud, Mtandari, Hughton, Fraser-Allen, Shehu (Kasim, 46), Mills, Hutton (Olsen, 60), Livermore, Pekhart, Hutchins, Obika. Unused sub: Medley.
Alex Inglethorpe was left scratching his head after our Under-18s were involved in an amazing climax to the FA Premier Academy League season.