Abstract Current global change scenarios demand knowledge on how anthropogenic impacts affect ecosystem functioning through changes in food web structure. Frugivorous mesocarnivores are a key link in trophic cascades because, while their abundance and behaviour are usually controlled by apex predators, they can provide high‐quality seed‐dispersal services to plant communities. Thus, the recent rewilding of large carnivores worldwide can trigger cascading effects for plants. We investigated the top‐down effects of an apex predator (Iberian lynx Lynx pardinus) on seed‐dispersal services mediated by two mesocarnivore species (red fox Vulpes vulpes and stone marten Martes foina) at the plant community level by comparing areas with and without lynx in a Mediterranean mountain range in Southern Spain. We collected scats of mesocarnivores (n = 1575) to assess frugivory and seed dispersal of 15 plant species over two consecutive fruiting seasons and two habitat types (open and forest). Specifically, we assessed the effect of lynx presence on (i) seed occurrence and fleshy‐fruit biomass per scat, (ii) number of scats containing seeds and (iii) diversity of dispersed seeds. The quantity and diversity of dispersed seeds drastically decreased under predation risk for both mesocarnivore's species. Seed dispersal by stone martens was negatively affected by the presence of lynx, with a marked reduction in the number of scats with seeds (93%) and the diversity of dispersed seeds (46%). Foxes dispersed 68% fewer seeds in open habitats when coexisting with lynx, probably leading to differential contributions to seed‐dispersal effectiveness among habitats. Our study reveals a novel trophic cascade from apex predators to plant communities. The behavioural responses of frugivorous mesocarnivores to predation risk and the reduction in the intensity of their faecal deposition pattern are probably related to their lower abundance when co‐occurring with apex predators. While rewilding apex predators is a successful conservation tool, attention should be paid to cascading effects across food webs, particularly where frugivore megafauna is missing and mesocarnivores provide unique services to plants. Read the free Plain Language Summary for this article on the Journal blog.