Bantams legend McCall, who was sacked in controversial circumstances 10 months ago and who took over The Iron in late August, was applauded all the way to his dugout.
But there the Christmas goodwill ended as Jack Payne and Eoin Doyle (penalty) struck before the break and Scunthorpe had interval substitute Cameron Burgess sent off in the 66th minute for two yellow cards.
City chief David Hopkin made two injury-enforced changes from the 4-0 win over Walsall. Doyle replaced Kelvin Mellor (knee) and Ryan McGowan came in for central defender Anthony O'Connor (gashed foot).
Former Bradford midfield player Josh Morris became the latest player to join Scunthorpe's lengthy injury list when he fractured a fibula in the 3-0 defeat at Scunthorpe. He will be out of action for the next two months but George Thomas recovered from a knee injury which forced him off after 17 minutes against Doncaster to take his place at Valley Parade.
The Iron made three changes with Funso Ojo, Levi Sutton and Kyle Wootton coming in for Matthew Lund, Morris and Andy Dales.
Richard O'Donnell made a flying save from Ojo in the opening minute but it was City who took a 10th-minute lead. Charlie Goode lost control near halfway and was robbed by Doyle, who fed Payne to his left. The Huddersfield loanee moved into the area and knocked the ball home off Jak Alnwick's left-hand post for his eighth goal of the campaign.
A lunging challenge on David Ball earned McArdle a booking in front of the Kop at a Scunthorpe corner and the visitors almost equalised when Lee Novak fed Thomas, who chipped the ball onto the roof of the net.
A blunder by McArdle, however, allowed Doyle to slam a 27th-minute penalty into the roof of the net. The Iron captain attempted to shield the ball back to Alnwick, only to be robbed by George Miller, who was brought down by the sprawling goalkeeper as the ball broke for Payne to hit into the net - after referee Carl Boyeson had awarded the penalty. Alnwick received only a yellow card before Doyle made it 2-0 from the spot.
Miller should have made it 3-0 but failed to connect with a whipped in cross from captain Paul Caddis.
More dawdling by the visitors saw Miller rob James Perch and knock the ball into the area where Doyle's shot deflected onto the bar and McArdle headed off the line.
Miller headed straight at the goalkeeper and forced a diving save from him and Ball shot into the side-netting after robbing Cameron Borthwick-Jackson before the break.
McArdle and Borthwick-Jackson paid the price, being replaced by defender Burgess and striker Ike Ugbo for the second half.
Ball curled an effort narrowly wide for City and Kyle Wootton volleyed over at the other end in the early stages.
Scunthorpe's hopes were ended as Burgess received two yellow cards in three minutes and was sent to the dressing room in the 66th minute.
Ball almost added to the visitors' woes with a shot on the turn but Alnwick beat it away for a corner before producing a series of saves to keep it at 2-0.
Kai Bruenker was City's first change in the 78th minute, replacing Miller and immediately heading over from a corner.
Scunthorpe's last change saw Clayton Lewis replace Thomas.
City were indebted to O'Donnell's outstretched right leg for keeping out a shot from Ojo and Wootton also looped a header narrowly off target.
Jim O'Brien was given a late run in place of the inspirational Payne and helped City close the game out in front of a 16,130 crowd.
There was also time for Eliot Goldthorp to make his league debut for City in the 90th minute.