Kelp species function as foundation organisms in coastal marine ecosystems, where they alter environmental conditions and promote local biodiversity by providing complex biogenic habitat for an array of associated organisms. The structure and functioning of kelp forest ecosystems in some regions, such as along the Peruvian coastline, remain critically understudied. We quantified the structure and diversity of faunal assemblages within both holdfast and understory reef habitats within Eisenia cokeri forests. We sampled both habitat types within four subtidal kelp forests on multiple occasions between 2016 and 2020, and quantified fauna at a fine taxonomic level (mostly species). We recorded a total of similar to 55,000 individuals representing 183 taxa across the study, with holdfast assemblages typically exhibiting higher richness, abundance and biomass values compared with understory reef-associated assemblages. Holdfast assemblages were structurally and functionally dissimilar to those on reef surfaces and were less variable and consistent across sites and sampling events. Even so, assemblages associated with both habitat types varied significantly between sites and sampling events, with variation in upwelling strength, ocean currents, and grazing pressure among potential drivers of this ecological variability. Overall, E. cokeri supports diverse and abundant holdfast assemblages and functions as a foundation organism in Peru. Given that no other habitat-forming kelp species persist at the low latitudes of E. cokeri in mid-to-north Peru, the lack of functional redundancy suggests that effective management and conservation of this species is vital for wider ecosystem processes and biodiversity maintenance.