Neil Danns then stung Gerken's hands with a low drive, as the visitors threatened to surge ahead before the break.
The keeper again denied Bolton soon after the restart with a smart save from Alex Baptiste's low drive.
Ipswich were awarded a penalty when Andy Lonergan brought down McGoldrick, who then duly converted to put the hosts in front.
The goal gave Ipswich confidence, with Jay Tabb firing a shot just over, as they established a period of dominance.
Neither side could add to the score, however, meaning that Ipswich secured all three points with a narrow win.