Cercle Bruges made a difficult start to the new Belgian Pro League season, losing 3-0 away to Westerlo four days before Kilmarnock visited on Thursday.
Miron Muslic’s side are considered favorites to progress to the third qualifying round of the Europa League after leaving Rugby Park with a 1-1 draw in the first leg.
But they will suffer from defeat to a team who finished 11th – seven places below them – in the national championship last season.
The home team, with Scottish Under-21 winger Dire Mebude in the starting line-up upon his return from last season’s loan spell at Bristol City, opened the scoring in the 18th minute, through Lucas Stassin.
The striker scored the second 10 minutes after the break and then set up striker Allahyar Sayyadmanesh just after the hour.
Muslic handed his debut to on-loan Red Bull Salzburg midfielder Lawrence Agyekum, while defender Boris Popovic and striker Filipe Augusto also started.
Former Ross County winger Kazeem Olaigbe, who scored Cercle’s goal in Ayrshire, Lithuanian midfielder Edgaras Utkus and striker Abdoul Quattara all went to the bench but came on as substitutes just before Westerlo’s third goal.