Goals from Leon Bailey, an own goal by Brandon Mechele, and a late penalty from Marco Asensio secured a solid victory for the Premier League side at Jan Breydelstadion.
Although the Villans have one foot in the quarter-finals, the Spaniard insists his team will take nothing for granted ahead of the second leg.
“There are still 90 minutes to play. We know their capacity. They won against Atalanta and they competed today very well,” Emery told the club website.
“The most important thing now is to watch the match again with the players and to understand the difficulties we can face in Europe against every team.
“Our experiences last year through Conference League was the same. I’m happy but calm. I’m taking balance because there are still 90 minutes to play.”
“We are ready in case we will need extra-time and a penalty shootout because I know how difficult it is in each match and how things can change with one match in 90 minutes.”
Before the second-leg clash against Club Brugge, Aston Villa will face Brentford on Saturday.