A moment of madness from Bolton keeper Andy Lonergan cost his team dear, after he hauled McGoldrick down in the 55th minute to gift Ipswich a penalty.
McGoldrick stepped up to hammer the spot-kick home and give Ipswich the three points they ultimately deserved.
It was often a scrappy game, with Bolton shading the first half but failing to lift their game after going a goal behind.
Five minutes in, McGoldrick got his first sniff at the target but he was unable to keep his far-post shot down after a teasing cross from Cole Skuse.
At the other end, Lukas Jutkiewicz, making his full debut following his loan move from Middlesbrough, was equally unable to find the target with a 12-yard header.
Bolton came a lot closer in the 12th minute when a searing break saw Tim Ream cross and Mark Davies fire wide, after initially mis-kicking.
A tight first 20 minutes came to life when Frank Nouble was put through by Stephen Hunt but his goalbound effort was blocked by Ream before the resulting corner was only partially cleared and Aaron Cresswell's 30-yard blockbuster was tipped over by Lonergan.
Bolton had their best chance in the 34th minute when Jay Spearing's through-ball found the onrushing Neil Danns but his poked effort was well saved by Dean Gerken's outstretched hand.
As the first half entered injury time, Jutkiewicz had Gerken sprawling across his goal but the shot from the edge of the area went just wide.
An insipid game livened up instantly after the interval, with Gerken saving smartly at his near post from Alex Baptiste after Christopher Berra had headed half-clear.
At the other end, sub Anthony Wordsworth fired over before Ipswich took the lead thanks to Lonergan's indiscretion.
A bout of head tennis ended with the Bolton keeper hauling down McGoldrick, with the stopper protesting the ball was in his hands first.
McGoldrick had missed his last two spot-kicks but this time he made no mistake, smashing the penalty straight down the middle for his 15th of the season.
And he almost made it 16 straight after, but flashed his shot wide of the far post.
The goal galvanised Ipswich, who had previously been below-par, and Hunt tried an audacious volley from 25 yards which Lonergan did well to hold low down to his left.
Bolton were offering little in the second half but Gerken was tested in the 82nd minute, but was again equal to it - Chris Eagles with the effort.