SCUNTHORPE ended Millwall's six-game unbeaten league run after Gary McSheffrey's goal in the first half and substitute Jim O'Brien's late strike gave them a deserved win at The Den.
The Iron could have gone ahead early on when Tom Hopper found space to turn six yards out but shot wide.
The away side went in front in the 17th minute when veteran McSheffrey finished left-footed past Jordan Archer from Stephen Dawson's pass.
Lee Gregory and then Jed Wallace tested Luke Daniels but the Scunthorpe goalkeeper was comfortably behind their efforts.
Millwall lost Ed Upson just before the break when he seemed to injure himself taking a free-kick that Gregory headed over. Ben Thompson came on for the midfielder.
Five minutes into the second half Daniels was quickly off his line to save from Aiden O'Brien.
Just before the hour mark Gregory thought he had dragged Millwall level after he ran onto Wallace's brilliant pass, but the striker was inches wide after lifting the ball over Daniels.
But Scunthorpe's O'Brien, who scored for Coventry at The Den earlier in the season, guaranteed the points for his new side in injury time.
Neil Harris mentioned the league positions of Leicester, Hull and Burnley as proof low possession stats don't necessarily mean a lowly status.
The message was perhaps with Millwall fans in mind, particularly at home, stressing the need for patience. After all, Millwall had more possession than Rochdale but less than Walsall, if only slightly, and won both games.
In the first half, though, the fans weren't that receptive to the idea. And with justification as Scunthorpe looked much more purposeful when they had possession and bullied their opponents off the ball when they didn't.
Just after Gregory had shot wide of Daniels' near post Millwall were in possession when they lost it, Dawson shifting the ball quickly to McSheffrey who inflicted maximum damage when he shot past Archer to the far post.
Millwall were often outnumbered and outfought in midfield in the opening 45 minutes, Dawson and Neal Bishop epitomising that with snarling performances that clearly set the tone for their teammates.
The home side actually shaded possession in the opening period, but as has been the case so often this season, not just in this game, it was the opposition who created the more clear-cut chances.
Dawson, as Bradley Dack had when Gillingham won 3-0 at The Den before Christmas, started at the attacking tip of a midfield diamond for Scunthorpe. In fact, Scunthorpe's formation was almost a 4-2-2-2 at times as they set out to dominate midfield.
Dawson has the shape of a boxer and at times the short temper of someone about to swing a punch, but he has a creative touch and possesses clever movement. Millwall had nothing like the same control, with Jimmy Abdou struggling to impose himself.
Thompson tried to give his side a more measured approach after the break, and Gregory was so close to levelling from that sumptuous Wallace through ball. The striker looked like he had done everything right but the ball bounced inches wide of Daniels' right-hand post.
But there was just not the same cohesion to Millwall's attacks as there was to Scunthorpe's. And, indeed, they did to their opponents what Millwall had done to Rochdale last weekend, slowing down and breaking up the play with experienced players like Bishop and David Mirfin taking their time getting to their feet after collisions. The frustration was very audible among the home fans.
Harris brought on John Marquis for Abdou as Millwall went all out to rescue at least a point. In the last minute of the 90 Byron Webster shot from inside the box but Daniels got down smartly to his left to save.
Millwall desperately tried to get the ball into their opponents' box as the clock ticked on, but instead it was Scunthorpe who kept their cool and the ball and after Archer had saved brilliantly from Bishop, O'Brien was there to slot home and send Millwall fans home wondering how it can be all so different from their performances on the road.
The Lions face Peterborough next Saturday. The Posh beat Millwall 5-3 in October in a frenetic contest, but the cavalier approach that characterised their displays when Graham Westley first took over have diminished slightly, not helped by the loss of Conor Washington.