Although Colin Larkin gave Chesterfield a 15th minute lead, Scunthorpe were transformed in the second half and moved to 50 points through goals from Richard Hinds and skipper Andy Crosby.
Chesterfield have now lost their last four home matches and once Crosby had given Scunthorpe the lead, they never threatened to salvage a point.
It had all looked so promising for the home side in the first half after they set off like a train, forcing five corners in the opening two minutes.
The swirling wind gave keeper Paul Musselwhite real problems and it was no surprise when he completely misjudged a cross from Kevan Hurst to gift Chesterfield the lead.
The ball sailed over the experienced keeper and bounced back off his left-hand upright to leave Larkin with a simple tap-in from inside the six-yard box.
Scunthorpe hardly figured as an attacking force before the break and their only consolation was that Chesterfield failed to make their superiority count with a second goal.
It was a different team that emerged for the second half, no doubt with a few well chosen words from manager Brian Laws to spur them on.
Andy Keogh should have equalised in the 47th minute when Steve Torpey put him through but he struck a post, but Chesterfield did not heed the warning signs and 60 seconds later Scunthorpe were level.
Keogh played the ball back to Michael Rose and the left-back nipped in a cross which Hinds met with a diving header from 12 yards to beat Rob Beckwith.
The keeper had an uncomfortable day on his debut following his loan move from Luton but could not be faulted for the goals and had good reason to question the defending in front of him for both.
The second was also a poor one from a Chesterfield viewpoint with Peter Beagrie drifting in a corner that Crosby guided inside the back post with a clever flick.
At least Beckwith had the confidence booster of a fine save minutes later that denied Keogh a goal when he plunged to his left to keep out a close-range header after Ian Baraclough had crossed.
But although their advantage was only a slender one, Scunthorpe never looked like losing the lead as Crosby led by example with a fine commanding defensive display.