Barker was youth-team boss when Scunthorpe manager Alan Knill was in charge at Gigg Lane and took the reins when Knill moved on to the Iron in March.
The former Sheffield Wednesday striker watched on as Scunthorpe raced into a fifth-minute lead as Michael O’Connor’s free-kick deflected off Shane Duffy and trickled in.
Andy Barcham would have made it 2-0 midway through the first half had it not been for a parrying save by Cameron Belford. O’Connor then saw an effort from the edge of the area come back off the crossbar.
However, the Shakers put in a fine second-half showing and bagged three goals to turn the game around. First Peter Sweeney levelled things up when he drilled in from 20 yards five minutes after the restart. Andy Bishop then sidefooted Bury ahead after 69 minutes after being set up by Mike Jones.
Efe Sodje headed a third late on to ensure Barker’s side took all three points. But the winning margin would have been even greater had it not been for a pair of superb saves from Sam Johnstone to deny Steven Schumacher and Sweeney late on.