1. Seed manipulation by ants can play a key role in seed germination through two main behaviours: elaiosome detachment and seed scarification. Despite the fact that these behaviours are commonplace, their effects have only been quantified independently, and their consequences on seed germination remain controversial.2. Here we experimentally investigate the effects of ant manipulation on seed germination, disentangling the contributions of these two ant behaviours to this process. To do so, under laboratory conditions, we studied the effects of seed manipulation by Acromyrmex subterraneus on germination of seeds from Mabea fistulifera, a myrmecochorous plant. We established six experimental treatments: (i) unmanipulated seeds; (ii) ant-manipulated seeds with the elaiosome detached and scarified; (iii) ant-manipulated seeds with the elaiosome detached and non-scarified; (iv) hand-manipulated seeds with the elaiosome remaining and scarified; (v) hand-manipulated seeds with the elaiosome detached and scarified; and (vi) hand-manipulated seeds with elaiosome detached and non-scarified.3. We found that both elaiosome detachment and seed scarification decreased seed germination rates. Moreover, there was no difference in germination rates whether the seeds were manipulated by researcher's hand or by ants, suggesting a lack of other ant-manipulation effects on seeds.4. The present study shows that manipulation by A. subterraneus can exert negative effects on germination of a myrmecochorous seed. Accordingly, we suggested that studies evaluating the benefits of myrmecochory for plants, based only on seed removal amount and distance, may be overestimating those benefits. Our results contribute to the understanding of the potential mechanisms influencing plant recruitment, especially for myrmecochorous plants inhabiting tropical forests.