Carbon storage is widely acknowledged as one of the most valuable forest ecosystem services. Deforestation, logging, fragmentation, fire, and climate change have significant effects on tropical carbon stocks; however, an elusive and yet undetected decrease in carbon storage may be due to defaunation of large seed dispersers. Many large tropical trees with sizeable contributions to carbon stock rely on large vertebrates for seed dispersal and regeneration, however many of these frugivores are threatened by hunting, illegal trade, and habitat loss. We used a large data set on tree species composition and abundance, seed, fruit, and carbon-related traits, and plant-animal interactions to estimate the loss of carbon storage capacity of tropical forests in defaunated scenarios. By simulating the local extinction of trees that depend on large frugivores in 31 Atlantic Forest communities, we found that defaunation has the potential to significantly erode carbon storage even when only a small proportion of large-seeded trees are extirpated. Although intergovernmental policies to reduce carbon emissions and reforestation programs have been mostly focused on deforestation, our results demonstrate that defaunation, and the loss of key ecological interactions, also poses a serious risk for the maintenance of tropical forest carbon storage. ; C.B., M.G., and R.A.F.L. thank the São Paulo Research Foundation (FAPESP) (grant nos. 2014/01986-0, 2013/22492-2, and 2013/08722-5). P.J. received financial support from Conselho Nacional de Desenvolvimento Científico (CNPq), Excellence Grant-Junta Andalucía. M.G. is a research fellow at Conselho Nacional de Desenvolvimento Científico e Tecnológico. P.J. is a visiting research fellow at CAPES (Programa Ciências Sem Fronteiras). L.F.S.M. was supported by Projeto Floresta Escola and by a postdoctoral grant from CAPES/PNPD. M.F.R. received a postdoctoral grant from Projeto Floresta Escola; O.O. was supported by the Academy of Finland (grant nos. 273523 and 284601). We acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI) ; Peer reviewed