The 48-year-old will be assisted by former Flames international Gerald Phiri, who last month was named interim coach, as well as Deklerk Msakakuona.
The Belgian has never worked in Africa before nor in international football.
"My target is to help the team rise on the Fifa rankings but the most important thing is that there is a good style of play," the Belgian said.
"I think that when you are a football coach you must live with pressure because everybody wants to win and that is also the same with me."
His first task will be later in April against Madagascar in the African Nations Championship, the tournament for locally-based players.
Malawi have been looking for a permanent coach since July last year the Football Association of Malawi (Fam) cut ties with Ernest Mtawali a month before the end of his contract.
"We are on a revival campaign to get back to winning ways and you know we are participating in the Africa Cup of Nations and CHAN competitions in the next year, so we want our performance to be better," Fam president Walter Nyamilandu said.
"We are meeting the African champions Cameroon, we are meeting Morocco who are coached by the two-time Africa Cup of Nations winner Herve Renard.
"For us to compete against the best in the world we need to have the right man behind the national team and that is why we said let us look for an expatriate coach."
The Fam president added that Malawi's results in the past two years have not been good and he believes Van Geneugden will turn things around.
"To turn around things for Malawi we needed new mentality and a new attitude and that what we believe the Belgian will help us achieve," he explained.
Van Geneugden was picked out of some 65 coaches and the highlight of his career so far was in 2010 when he helped Heverlee Leuven to promotion into the topflight of Belgian football.
In a change from the past Fam will cover Van Geneugden's salary rather than the government, who have said they can no longer pay a foreign coach's wages.
Belgian Ronny Van Geneugden has been appointed as the new coach of Malawi on a two-year deal.