Placement of seeds in favourable microsites by inhumation in ant nests is considered a principal advantage of myrmecochory. However, nest chambers may be too deep to allow seedling emergence. In this case, successful germination requires secondary transport of seeds to shallower sites. Little is known about the architecture of nests of seed-dispersing ants and the locations within nests to which seeds are initially transported. These data are essential to assess the importance of secondary transport for germination success of seeds. We studied dispersal of Manihot esculenta subsp. flabellifolia seeds by Ectatomma brunneum ants in French Guianan savannas. We followed movements of seeds within nests by offering marked diaspores to foraging workers, observing transport into the nest, then excavating to determine locations of marked seeds. In 4 nests, chambers ranged from 2 to 40 cm deep. Because elaiosomes are fed to brood, Manihot diaspores were initially transported to deep chambers, where brood was concentrated. Recovered diaspores had been carried to chambers 14–40 cm deep, all deeper than the maximum burial depth for emergence (≈ 13.8 cm) predicted from the mass (≈ 0.13 g) of Manihot seeds. Nest architecture thus makes secondary vertical transport of seeds crucial for dispersal success of this species. Failure of secondary transport may be an underestimated mortality factor in myrmecochorous plants.