Although large crabs are recognized as important sediment disturbers influencing the structure of benthic communities, the role of dominant predatory crabs in soft-bottom habitats along the Humboldt Current Ecosystem, remains largely unknown. A field study was conducted, hypothesizing that the digging activity of these predators disturbs the habitat thereby leading to a reduction in individual abundance, biomass and species richness; these changes result in a modified structure of macrobenthic communities. A directed sampling (crab pits vs. reference areas) showed significant reductions in total abundances in pits compared to reference areas, but no differences were observed in taxonomic richness or benthic biomass. Short-term cage experiment showed significant decreases in total abundance and biomass of macroinvertebrates in predator inclusion treatments compared to exclusions and controls. In consequence, our results confirmed that burrowing activities and the generation of small disturbed sediment patches influence the community structure. These results highlight the importance of large cancrid crabs in soft-bottom habitats, where their modification of the physical configuration of the sediment affects community structure over small spatial scales. Crabs are thus an important source of spatial heterogeneity of the sea-floor landscape. This ecological role must be considered in management strategies of the extensive artisanal fishery for these crabs, as current evidence is showing increasing populations of intermediate predators (like cancrid crabs) in many benthic habitats in response to the depletion of top predators. © 2013 Elsevier B.V.