Scunthorpe had most of the chances but never quite found top gear against the well-organised visitors, for whom goalkeeper Ross Worner was in excellent form.
The Dons, with only one win in their previous nine games, threatened to turn the form book upside down in the early stages despite losing centre-back Andy Frampton through injury.
Striker Charlie Wyke twice came close to opening the scoring, first with a long-range shot which tested 'keeper Sam Slocombe, then with a far-post header from a corner which flashed into the side-netting.
When Scunthorpe began to get into their stride it was leading marksman Sam Winnall whose finishing let him down. Three times he got free into the box but each time he was denied by 'keeper Worner.
It was man of the match Worner who denied Winnall again from close range in the second half as Scunthorpe stepped up the pressure.
David Syers and Paul Hayes both fired just wide but AFC Wimbledon stuck manfully to their task to frustrate the home side.
Scunthorpe brought on new striker Paddy Madden for his home debut as part of a double substitution late in the game, but he got little chance to impress.