As a manager, Van Geneugden had most of his successes with Oud-Heverlee Leuven, leading them to the Belgian Second Division title in 2010–11, hence gaining promotion to the 1st division for season 2011–12, he was rewarded with a contract extension to 2015.[1] Despite two successful seasons in the 1st division where Oud-Heverlee Leuven finished mid-table, his contract was terminated on 21 January 2014 as his team sat second bottom of the 1st division after a poor first half of the 2013–14 season.[2]
In April 2017, Van Geneugden signed a 2-year-deal in Malawi as the head coach of the national team. The contract expired on 31 March 2019 and on 6 April 2019, the Football Association of Malawi announced that the contract would not be renewed.[3][4]