City will take a two goal advantage to Denmark next week thanks to first half strikes from Felipe Caicedo and Shaun Wright-Phillips.
But it could have been more. Indeed, had the Blues scored five their visitors could not have complained such was the one-sided nature of the contest.
It leaves City with work to do in seven days time but Hughes believes they are up to the task.
"Ideally we would like to have put the game to bed," he said.
"We had enough chances to score more than we did. But we got a positive result and a clean sheet and overall it was a very good European performance.
"Aalborg have to attack us now. I am sure that will provide us with opportunities and if we play as well next week as we did here it will be very difficult for them."
Once again, Wright-Phillips was the star man but the England winger was not on his own. Even without midfield duo Vincent Kompany and Nigel de Jong, the hosts had top performers across the field.
The win leaves City on the brink of their first appearance in a European quarter-final for 30 years and one Hughes is convinced they will take.
"We are in good shape," said the City boss.
"The aim has always been to get through to the next round. Once you get through to the quarters and semi-finals then you can start thinking about winning the whole thing."
Before City head to Denmark for the third time in this competition they have the little matter of Chelsea to face at Stamford Bridge on Sunday.
It hardly seems the ideal venue to end a winless Premier League away sequence stretching back to August. But Hughes is quietly optimistic.
"It is a big test for us but one we are looking forward to," he said.