Facultative ant–plant mutualisms are variable systems, shaped by a number of biotic and abiotic factors. Especially in tropical ecosystems, the generally assumed mutualistic benefits are often hard to prove. We studied the system Leea manillensis on the Philippine island Panay and its indirect defence mechanism against herbivory by producing extrafloral nectar therewith attracting ants. Unexpectedly, we found an ant-parasitoid wasp from the genus Chalcura (Eucharitidae) to have a strong influence on the system, on ants as well as on plants. The parasitoid not only altered the behaviour of interacting ant species, but also directly and indirectly affected the plants’ fitness. This study demonstrates how top-down effects may alter species interactions and have a massive effect on mutualisms and their beneficial outcome.