Plymouth Argyle ended the Central League campaign in fourth position after a side of young professionals and apprentices lost 3-2 away to Forest Green Rovers on Tuesday.
It meant the Pilgrims ended the season without winning any of their last six games in the development squad competition.
MK Dons were confirmed as champions after their 3-2 home win against Peterborough United, also on Tuesday.
Academy director Kevin Hodges and coach Robbie Herrera took charge of Argyle against Forest Green.
They took on the responsibility after the elevation of Kevin Nancekivell to caretaker manager of the first team following the departure of Derek Adams.
Goalkeeper Michael Cooper was also an absentee from the squad which travelled to play the fixture at Stanley Park, Chippenham.
Cooper was an unused substitute for the first team when they were thrashed 5-1 at Accrington Stanley on Saturday.
Matt Macey was between the posts in that game because of an injury to Kyle Letheren.
The fact that Cooper did not play against Forest Green would hint at the possibility that Letheren will not be fit for the season-ending League One visit of Scunthorpe United either.
Argyle opened the scoring at Stanley Park with a goal from midfielder Dan Rooney.
Fresh from a successful loan spell at Truro City, the midfielder fired home from a tight angle in the 13th minute.
Sam Hendy equalised for Forest Green shortly before half-time and the hosts then went 3-1 up with goals from Dan Ogunleye and Oliver Artwell in the 65th and 70th minute respectively.
Wales under-19 international Luke Jephcott replied for Argyle soon afterwards, beating ‘keeper Lewis Thomas from 25 yards out.
However, the young Pilgrims could not get on level terms as Forest Green, managed by former Argyle left-back Chris Barker, held on.
It was their fourth Central League win of the campaign and lifted them off the bottom of the table.
Argyle, in fourth, finished behind MK Dons, runners-up Exeter City and AFC Wimbledon.
Argyle: Tyler Coombes; Isaac Burdon, Mike Peck, Ollie Tomlinson, Harry Hodges (Rio Garside h/t); Cameron Sangster, Adam Randall, Dan Rooney; Aaron Goulty (Jarvis Cleal 89 mins), Klaidi Lolos, Luke Jephcott.
Substitutes (not used): Harry Townsend, Andy Burn, Tom Purrington.