Matthew Sparrow returned from suspension to have a major influence on the game with a brace of goals while Richard Kell was a key figure in both defence and attack.
Jamie Victory was a solid figure for he Robins and deserved his goal - and, if Steve Guinan had accepted a fairly easy chance in the first-half, it might have had an effect on the result.
Cheltenham opened strongly and inside 10 minutes David Bird and Brian Wilson forced Paul Musselwhite into a save.
However from there on they were under pressure as Scunthorpe dominated proceedings with midfielder Kell forcing Shane Higgs to palm a shot over and then concede a second corner.
Steven Gillespie caught Scunthorpe's centre-back Stevland Angus in possession and he forced the ball through for Guinan who should have done better than blaze wildly over.
Kell was again in the action with an excellent 30-yard drive which Higgs saved at the foot of his left-hand post.
In a rare Cheltenham raid Gillespie headed over but it was the home side that kept up the pressure as Peter Beagrie fired a free-kick inches wide.
Scunthorpe broke the deadlock after 44 minutes. A quickly taken free-kick saw a Paul Hayes pushed away by Higgs to give Matthew Sparrow an easy tap in.
Within three minutes of the restart the Robins were level when, following a free-kick, Jeremy Gill knocked the ball into the middle and Gavin Caines challenged Musselwhite, who failed to gather and the ball fell to Victory who fired home.
Scunthorpe regained the lead in the 56th minute, a mix up between Higgs and Grant McCann following a Hayes cross saw Steve Torpey flick the ball on for Sparrow to knock home his second.
Cheltenham were not quite a spent force and when the powerful Victory hammered in a cross from the left John Finnigan's header forced Musselwhite to save at full stretch.
However Scunthorpe reasserted themselves in the closing stages with great effect and Kell, who had been an inspiration all afternoon, whipped in a superb angled shot in the 85th minute.
And five minutes later defender Cliff Byrne took advantage of a half cleared corner to make it four, for the Irons best home win of the campaign.