Ian Evatt's side might wonder how the win wasn't more comfortable given their overall dominance.
But after Scunthorpe took advantage of Bolton's first-half profligacy to end the opening period strongly, the response was impressive, and a sure sign of a side growing in confidence.
Peter Kioso's goal was the difference, and it was a finish worthy of winning any game.
Having started the move himself on the halfway line, he then took the ball back off Nathan Delfouneso and fired into the bottom corner.
And it was no more than they deserved.
Bolton started brightly, winning a corner virtually from the kick-off which Ryan Delaney would have been disappointed to flick over after stooping to meet Ali Crawford's delivery at the near right post.
Eoin Doyle would have been just as frustrated not to test former Wanderers stopper Mark Howard in the Iron goal soon after when Jacob Bedeau misjudged a long ball forward and it bounced kindly for the in-form striker, but his shot sailed over the bar.
Bolton built on their positive opening and Kioso delivered a dangerous ball into the box. It just needed the slightest of touches at the far left post, but Gethin Jones couldn't get the necessary connection to steer it home and instead it dropped wide.
There was more frustration when a big penalty appeal fell on deaf ears when Doyle went down under a challenge as he got Crawford's pass under control in the box.
Scunthorpe made inroads for the first time 10 minutes into the game, but Junior Brown's effort was so far off target it went out for a throw-in and Bolton came back at the home side with Antoni Sarcevic forcing a good save from Howard with his low strike after a throw-in on the right.
The ball bounced awkwardly in front of the ex-Bolton man, who did well to keep it out, producing another excellent save to deny Delfouneso's curling right-foot shot moments later. Doyle was poised and ready to pounce on any rebound or spillage, but Howard did not let the ball leave his grasp.
The striker's frustration showed when he rushed a chance when he had time and other options. But he was a menace to the home side, continually getting into good areas and utilising the confidence of his recent scoring streak.
But without a goal to show for their possession and pressure it allowed Scunthorpe to grow into the game, and after Abo Eisa went close with a free kick around the half-hour mark, the Iron ended the half strongly.
The home side, managed by former Bolton defender Neil Cox, looked particularly dangerous at set pieces and when Eisa curled another delivery into the box it needed the experienced head of Alex Baptiste to steer it to safety with a header behind.
From the corner, Emmanuel Onariase was unlucky to miss the target with a glancing header after Bedeau had flicked on.
Despite bossing the first half-hour there was perhaps relief in the Wanderers dressing room that they had got to the break goalless given Scunthorpe's late flourish.
Evatt would not have needed to warn of the consequences of missed chances, they have been hurt by them before this season, and they started the second half with renewed vigour.
Crawford whipped in a terrific delivery but it somehow missed everyone in a packed penalty box.
But it was a sign of things to come, although they had some defending to do first, which Ricardo Santos did well.
From there, Kioso picked up the ball on the halfway line and triggered the move he finished. The wide man fed Delfouneso, who skipped past two defenders before returning the ball to the wing back, who fired past Howard.
Matt Gilks made a couple of good saves to preserve the lead - one low to his left from Eisa, the other clawing out John McAtee's cross-shot that threatened to dip under the bar - but his role was otherwise one of a conductor, organising everyone in front of him.
Kioso could have put the result beyond doubt with a free header, but Bolton had enough quality to secure the win regardless.
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