All the pre-match talk centred on the future of Nigel Adkins, but with the Iron and League One Southampton yet to agree terms on compensation he remained in the dugout at Glanford Park.
The Iron opened brightly, clearly intent on sending off Adkins on a high. Sam Togwell brought a great save out of David James, City's goalkeeper who represented England in the World Cup, with a half-volley after six minutes.
Michael O'Connor also sent a shot narrowly wide, but the visitors took the lead after 16 minutes when the Iron gave the ball away cheaply with a quickly-taken free-kick.
With the Iron's centre-backs heading upfield for the set-piece, they quickly had to rush back as Albert Adomah - a former target for the Iron - brought the ball up the field. He played a one-two with Brett Pitman and struck the ball past Joe Murphy.
Heads fell in the home team, who soon had to send on Niall Canavan in place of the injured Rob Jones.
Adkins had said before the match that players would not be affected by speculation over his future, and while it is hard to say if it had an impact the last half hour of the first-half was poor.
They repeatedly gave the ball back to the Robins and lacked confidence or composure on the ball. Scunthorpe did not create any clear chances, with Pitman blasting the ball way off target when he should have doubled the lead.
The second-half was a different story for the Iron, who controlled possession but struggled to create clear-cut chances.
One of the best opportunities was a free-kick from O'Connor, which was deflected off the defensive wall and just over the bar as James stood helpless.
Jonathan Forte had much of the ball. He often dribbled past four or five visiting defenders, but by the time he got a shot away there was usually an opponent's leg in the way.
Forte created the best chance of the second-half when he won a header to flick the ball on to Chris Dagnall, whose first-time shot went just over the bar.
Martyn Woolford and Bobby Grant came off the bench as Adkins adopted a more attacking approach, but that left gaps at the back which City managed to exploit in second-half stoppage time when David Clarkson scored after Jonathan Stead's flick-on.